DISI - User contributions [en]

How to dock in DOCK3.8

2021-02-03T00:46:15Z

Stefan:

How to dock in DOCK 3.8.0

== Differences from DOCK.3.7 ==

DOCK 3.8.0 can be interrupted safely and restarted, which allows more flexibility when submitting docking jobs.

For example, you could set QSUB_ARGS="-l s_rt=00:05:00 -l h_rt=00:07:00" (or SBATCH_ARGS="--time=00:07:00")
so that each docking job will only run for 5 minutes before being interrupted. The new subdock.bash script allows submitting the same set of jobs multiple times, until they are all complete.

== Running the Script ==

New subdock scripts are here:

$DOCKBASE/docking/submit/sge/subdock.bash
$DOCKBASE/docking/submit/slurm/subdock.bash

subdock.bash requires a number of environmental variables to be passed as arguments.

=== Required Arguments ===

==== INPUT_SOURCE ====

INPUT_SOURCE should be either:

a) A directory containing one or more db2.tgz files OR

b) A text file containing a list of paths to db2.tgz files

==== EXPORT_DEST ====

A directory on the NFS where you would like your docking output to end up. If the directory does not exist, the script will try to create it.

==== DOCKEXEC ====

An NFS path to a DOCK binary executable (NOT a wrapper script).

==== DOCKFILES ====

An NFS path to the dockfiles (INDOCK, spheres, receptor files, grids, etc.) being used for this docking run. The dockfiles directory should be named uniquely, to avoid confusion with other dockfiles other users may be running.

=== Optional Arguments ===

==== SHRTCACHE ====

The directory DOCK will perform it's work in. Files saved to this directory will be deleted once the docking job has concluded. By default this is /dev/shm.

==== LONGCACHE ====

The directory DOCK will store files that are shared between multiple docking jobs. Files saved to this directory (dockexec and dockfiles) will persist until they are deleted. By default this directory is /tmp.

Beware of using the default SHRTCACHE or LONGCACHE settings on large clusters.

==== SBATCH_ARGS ====

Additional arguments to provide to slurm's sbatch, if using the slurm version of subdock.bash.

==== QSUB_ARGS ====

Additional arguments to provide to sge's qsub, if using the sge version of subdock.bash

=== Example: Running a lot of docking jobs ===

* 1. set up sdi files
mkdir sdi
export sdi=sdi
ls /wynton/group/bks/zinc-22/H19/H19P0??/*.db2.tgz > $sdi/h19p0.in
ls /wynton/group/bks/zinc-22/H19/H19P1??/*.db2.tgz > $sdi/h19p1.in
ls /wynton/group/bks/zinc-22/H19/H19P2??/*.db2.tgz > $sdi/h19p2.in
ls /wynton/group/bks/zinc-22/H19/H19P3??/*.db2.tgz > $sdi/h19p3.in
and so on

* 2. set up INDOCK and dockfiles. rename dockfiles to dockfiles.$indockhash. On some nodes, the shasum command is called by sha1sum. Ultimately, renaming the dockfiles to a unique dockfiles is key.
bash
indockhash=$(cat INDOCK | shasum | awk '{print substr($1, 1, 12)}')

* 3. super script:

<nowiki>
export DOCKBASE=/wynton/group/bks/work/jji/DOCK
export DOCKFILES=$WORKDIR/dockfiles.21751f1bb16b
export DOCKEXEC=$DOCKBASE/docking/DOCK/bin/dock64
#export SHRTCACHE=/dev/shm # default
export SHRTCACHE=/scratch
#export LONGCACHE=/scratch # default
export QSUB_ARGS="-l s_rt=00:28:00 -l h_rt=00:30:00 -l mem_free=2G"

for i in sdi/*.in ; do
export k=$(basename $i .in)
echo k $k
export INPUT_SOURCE=$PWD/$i
export EXPORT_DEST=$PWD/output/$k
$DOCKBASE/docking/submit/sge/subdock.bash
done
</nowiki>

# 3a. to run for first time
sh super

# 4. how to restart (to make sure complete, iterate until complete)

sh super

# 5. check which output is valid (and broken or incomplete output)

# 6. extract all blazing fast

# 7. extract mol2

more soon, under active development, Jan 28.

Flexible Docking: tarting and thin spheres

2020-12-31T02:14:14Z

Stefan:

written by Stefan Gahbauer 12/30/2020

Weighted flexible docking as described in Fischer ''et al.'', Nat. Chem., 2014 [https://www.nature.com/articles/nchem.1954], is implemented in DOCK3.7, however, fine-tuning docking grids using tarting or thin spheres was not possible with the common scripts used for rigid docking.

== Run flexible blastermaster on protonated rec.crg.pdb including tarted residues ==

DOCKBASE with adapted blastermaster_flex function:

/mnt/nfs/exc/work/stefan/Flexible_docking_Tarting_Thin_Spheres/DOCK-3.7.4-1228

This version cannot be used to protonate rec.pdb, rec.crg.pdb containing protonated flexible states must be prepared before.

You can find an example for AmpC with tarted, flexible GLN120 here:

/mnt/nfs/exc/work/stefan/exc/Flexible_docking_Tarting_Thin_Spheres/example_AmpC

Run blastermaster for flexible grid generation:

python /mnt/nfs/exc/work/stefan/Flexible_docking_Tarting_Thin_Spheres/DOCK-3.7.4-1228/proteins/blastermaster/blastermaster.py
--addNOhydrogensflag -v -f --flexiblePenaltyM=2.0 --flexibleResidues=120
--chargeFile="/nfs/home/stefan/exc/Flexible_docking_Tarting_Thin_Spheres/example_AmpC/amb.crg.oxt"
--vdwprottable="/nfs/home/stefan/exc/Flexible_docking_Tarting_Thin_Spheres/example_AmpC/prot.table.ambcrg.ambH"

This will generate INDOCK, dockfiles for flexible docking, flexible.explanation.txt and part.explanation.txt.

== Thin sphere scan ==

After the initial grids are computed with blastermaster, thin spheres can be introduced by using the following script:

/mnt/nfs/exc/work/stefan/Flexible_docking_Tarting_Thin_Spheres/thin_sphere_scan/new_0001_generate_ES_LD_generation_flexible.py

This script is based on the rigid-docking thin sphere scan by Reed: [http://wiki.docking.org/index.php/How_to_do_parameter_scanning]
A few new options were added for flexible thin sphere scans:

usage: new_0001_generate_ES_LD_generation_flexible.py [-h]

This is a sphere scan directory generator script. This script requires that
you provide the full path to your original blastermaster directory that you
want to run a sphere scan on. This looks like: python
new_0001_generate_ES_LD_combine.py --path
/mnt/nfs/blah/work/yourName/blah/DOCKprep/ Other options include specifying
the: 1) DMS density (--dms) 2) electrostatic thin sphere radii (--es_rad) 3)
ligand desolvation sphere radii (--ld_rad) 4) distance of spheres to your
xtal-lig.pdb (--xdist) 5) Grid IDs (--flexgrids) 6) Ground state grid
(--ground_state)

optional arguments:
-h, --help show this help message and exit
-p ORI_PATH, --path ORI_PATH
Full path of the original blastermaster directory,
e.g. /mnt/nfs/work/asdf/asdf/asdf/
-d DMS, --dms DMS DMS Density. The higher the number, the more dense the
molecular surface is. 10.0 is default to ensure that
the smaller radii spheres sufficiently cover the
protein surface. If your spheres have larger radii or
if you are using small radii for ES spheres and QNIFFT
fails, this value can be decreased to 1.0.
-es ES_RAD [ES_RAD ...], --es_rad ES_RAD [ES_RAD ...]
Radius of Electrostatic spheres.
Default is 1.0, 1.3, 1.5, 1.7, 1.9
-ld LD_RAD [LD_RAD ...], --ld_rad LD_RAD [LD_RAD ...]
Radius of ligand desolvation spheres.
Default is 0.1, 0.2, 0.3, 0.4, 0.5
-xd XDIST, --xdist XDIST
Distance thin spheres can be from xtal-lig.pdb.
Default is 2 Angstroms
'''-fg GNUM [GNUM ...], --flexgrids GNUM [GNUM ...]'''
'''Alternative conformation names. E.g. A,B,C'''
'''-gs GROUND_STATE, --ground_state GROUND_STATE'''
'''Ground state conformation name. E.g. A'''

Example:

python /mnt/nfs/exc/work/stefan/Flexible_docking_Tarting_Thin_Spheres/thin_sphere_scan/new_0001_generate_ES_LD_generation_flexible.py
-p /nfs/home/stefan/exc/Flexible_docking_Tarting_Thin_Spheres/example_AmpC
-d 5 -es 1.0 1.5 1.9 -ld 0.4 0.6 0.8 -xd 4
-fg A B C -gs A

This will take a few minutes (code is still being optimized).

Once the girds are calculated, dockfiles for different thin sphere combination need to be generated using the following script:

/mnt/nfs/exc/work/stefan/Flexible_docking_Tarting_Thin_Spheres/thin_sphere_scan/new_0002_combine_es_ld_grids_into_combos_flexible.py

usage: new_0002_combine_es_ld_grids_into_combos_flexible.py
[-h] -p ORI_PATH -fg GNUM [GNUM ...] -gs GROUND_STATE

This is a sphere scan directory generator script. This script requires that
you provide the full path to your original blastermaster directory that you
want to run a sphere scan on. This looks like: python
new_0002_combine_ES_LD.py --path /mnt/nfs/blah/work/yourName/blah/DOCKprep/
--flexgrids A B C --ground_state A

optional arguments:
-h, --help show this help message and exit
-p ORI_PATH, --path ORI_PATH
Full path of the original blastermaster directory,
e.g. /mnt/nfs/work/asdf/asdf/asdf/
'''-fg GNUM [GNUM ...], --flexgrids GNUM [GNUM ...]'''
'''Alternative conformation names. E.g. A,B,C'''
'''-gs GROUND_STATE, --ground_state GROUND_STATE'''
'''Ground state conformation name. E.g. A'''

Example:

python /mnt/nfs/exc/work/stefan/Flexible_docking_Tarting_Thin_Spheres/thin_sphere_scan/new_0002_combine_es_ld_grids_into_combos_flexible.py
-p /nfs/home/stefan/exc/Flexible_docking_Tarting_Thin_Spheres/example_AmpC
-fg A B C -gs A

This will generate combo_directories containing flexible docking grids.

Flexible Docking: tarting and thin spheres

2020-12-31T02:00:32Z

Stefan: Created page with "written by Stefan Gahbauer 12/30/2020 Weighted flexible docking as described in Fischer ''et al.'', Nat. Chem., 2014 [https://www.nature.com/articles/nchem.1954], is implemen..."

written by Stefan Gahbauer 12/30/2020

Weighted flexible docking as described in Fischer ''et al.'', Nat. Chem., 2014 [https://www.nature.com/articles/nchem.1954], is implemented in DOCK3.7, however, fine-tuning docking grids using tarting or thin spheres was not possible with the common scripts used for rigid docking.

== Run flexible blastermaster on protonated rec.crg.pdb including tarted residues ==

DOCKBASE with adapted blastermaster_flex function:

/mnt/nfs/exc/work/stefan/Flexible_docking_Tarting_Thin_Spheres/DOCK-3.7.4-1228

This version cannot be used to protonate rec.pdb, rec.crg.pdb containing protonated flexible states must be prepared before.

You can find an example for AmpC with tarted, flexible GLN120 here:

/nfs/home/stefan/exc/Flexible_docking_Tarting_Thin_Spheres/example_AmpC

Run blastermaster for flexible grid generation:

python /mnt/nfs/exc/work/stefan/Flexible_docking_Tarting_Thin_Spheres/DOCK-3.7.4-1228/proteins/blastermaster/blastermaster.py
--addNOhydrogensflag -v -f --flexiblePenaltyM=2.0 --flexibleResidues=120
--chargeFile="/nfs/home/stefan/exc/Flexible_docking_Tarting_Thin_Spheres/example_AmpC/amb.crg.oxt"
--vdwprottable="/nfs/home/stefan/exc/Flexible_docking_Tarting_Thin_Spheres/example_AmpC/prot.table.ambcrg.ambH"

This will generate INDOCK, dockfiles for flexible docking, flexible.explanation.txt and part.explanation.txt.

== Thin sphere scan ==

After the initial grids are computed with blastermaster, thin spheres can be introduced by using the following script:

/mnt/nfs/exc/work/stefan/Flexible_docking_Tarting_Thin_Spheres/thin_sphere_scan/new_0001_generate_ES_LD_generation_flexible.py

This script is based on the rigid-docking thin sphere scan by Reed: [http://wiki.docking.org/index.php/How_to_do_parameter_scanning]
A few new options were added for flexible thin sphere scans:

usage: new_0001_generate_ES_LD_generation_flexible.py [-h]

This is a sphere scan directory generator script. This script requires that
you provide the full path to your original blastermaster directory that you
want to run a sphere scan on. This looks like: python
new_0001_generate_ES_LD_combine.py --path
/mnt/nfs/blah/work/yourName/blah/DOCKprep/ Other options include specifying
the: 1) DMS density (--dms) 2) electrostatic thin sphere radii (--es_rad) 3)
ligand desolvation sphere radii (--ld_rad) 4) distance of spheres to your
xtal-lig.pdb (--xdist) 5) Grid IDs (--flexgrids) 6) Ground state grid
(--ground_state)

optional arguments:
-h, --help show this help message and exit
-p ORI_PATH, --path ORI_PATH
Full path of the original blastermaster directory,
e.g. /mnt/nfs/work/asdf/asdf/asdf/
-d DMS, --dms DMS DMS Density. The higher the number, the more dense the
molecular surface is. 10.0 is default to ensure that
the smaller radii spheres sufficiently cover the
protein surface. If your spheres have larger radii or
if you are using small radii for ES spheres and QNIFFT
fails, this value can be decreased to 1.0.
-es ES_RAD [ES_RAD ...], --es_rad ES_RAD [ES_RAD ...]
Radius of Electrostatic spheres.
Default is 1.0, 1.3, 1.5, 1.7, 1.9
-ld LD_RAD [LD_RAD ...], --ld_rad LD_RAD [LD_RAD ...]
Radius of ligand desolvation spheres.
Default is 0.1, 0.2, 0.3, 0.4, 0.5
-xd XDIST, --xdist XDIST
Distance thin spheres can be from xtal-lig.pdb.
Default is 2 Angstroms
'''-fg GNUM [GNUM ...], --flexgrids GNUM [GNUM ...]'''
'''Alternative conformation names. E.g. A,B,C'''
'''-gs GROUND_STATE, --ground_state GROUND_STATE'''
'''Ground state conformation name. E.g. A'''

Example:

python /mnt/nfs/exc/work/stefan/Flexible_docking_Tarting_Thin_Spheres/thin_sphere_scan/new_0001_generate_ES_LD_generation_flexible.py
-p /nfs/home/stefan/exc/Flexible_docking_Tarting_Thin_Spheres/example_AmpC
-d 5 -es 1.0 1.5 1.9 -ld 0.4 0.6 0.8 -xd 4
-fg A B C -gs A

This will take a few minutes (code is still being optimized).

Once the girds are calculated, dockfiles for different thin sphere combination need to be generated using the following script:

/mnt/nfs/exc/work/stefan/Flexible_docking_Tarting_Thin_Spheres/thin_sphere_scan/new_0002_combine_es_ld_grids_into_combos_flexible.py

usage: new_0002_combine_es_ld_grids_into_combos_flexible.py
[-h] -p ORI_PATH -fg GNUM [GNUM ...] -gs GROUND_STATE

This is a sphere scan directory generator script. This script requires that
you provide the full path to your original blastermaster directory that you
want to run a sphere scan on. This looks like: python
new_0002_combine_ES_LD.py --path /mnt/nfs/blah/work/yourName/blah/DOCKprep/
--flexgrids A B C --ground_state A

optional arguments:
-h, --help show this help message and exit
-p ORI_PATH, --path ORI_PATH
Full path of the original blastermaster directory,
e.g. /mnt/nfs/work/asdf/asdf/asdf/
'''-fg GNUM [GNUM ...], --flexgrids GNUM [GNUM ...]'''
'''Alternative conformation names. E.g. A,B,C'''
'''-gs GROUND_STATE, --ground_state GROUND_STATE'''
'''Ground state conformation name. E.g. A'''

Example:

python /mnt/nfs/exc/work/stefan/Flexible_docking_Tarting_Thin_Spheres/thin_sphere_scan/new_0002_combine_es_ld_grids_into_combos_flexible.py
-p /nfs/home/stefan/exc/Flexible_docking_Tarting_Thin_Spheres/example_AmpC
-fg A B C -gs A

This will generate combo_directories containing flexible docking grids.

Quartzy and BearBuy

2020-08-04T21:51:25Z

Stefan:

Compounds are typically ordered by adding requests on quartzy.com. Once the request is approved, the order is placed on BearBuy (by the lab manager). Here are a few things to keep in mind.

= Placing requests and adding new vendors to BearBuy =

'''1)''' Whenever possible, if the lab still uses Quartzy, please enter (not place orders via Quartzy) your orders in Quartzy vs sending them directly to the lab manager (Henry). Entering it in Quartzy will help keep track of the whereabouts of the compounds you are ordering (qty, location, etc).
Henry will check Quartzy & place your orders.

'''2)''' If a vendor is not set up in BearBuy, have the vendor complete the '''W-8BEN-E''' form (for international vendors), or, the '''W-8BEN''' form (for domestic vendors). To check whether a vendor is setup in BearBuy, login via MyAccess and search through the suppliers.
The W8 forms are available from the purchasing manager Matthew Denny (matt.denny@ucsf.edu). Forward the completed form to Yvonne or Matt Denny so the vendor can be set up in BearBuy.

'''3)''' Please DO NOT place orders w/o PO #s, or, have vendors invoice UCSF w/o a PO #. An order, or, invoice w/o a PO # causes problems w/ purchasing & accounting. Don't place orders w/o PO #s. If you have an urgent order, you will still need a PO to place it. If necessary, consult Matt Denny (matt.denny@ucsf.edu) on how to best place/expedite urgent orders, or, if you have any questions about purchasing.

= Placing orders in BearBuy from Quartzy requests =

Written by Henry O'Donnell

=== How to place orders for the lab ===

- Log in to Quartzy and check for new order requests, take note of the total price, the supplier, name of the person who placed the order, and the grant ID

If there is a PDF quote attached for multiple compounds:

-Click on the order request and download the PDF, but rename the file by adding the requester’s name and the date. For Example, change “Q125768.pdf” to “John Smith March 2 Q125768.pdf”

-Copy the new file name (exclude .pdf), in this example you would copy “John Smith March 2 Q125768”

-Log in to MyAccess and open “BearBuy”, scroll down and select “Amount based PO”

-Input the name of the supplier (if the supplier is Tocris, input R&D)

-Under Product description write “Chemicals per attached quote John Smith March 2 Q125768”. Paste the name of the file to save time and avoid mistakes.

-Input the total price, select commodity code 00025 Chemicals, select “No” for the Protected health drop down, “No” for the services requested drop down, and “Agree” for the conflict of interest question

-Scroll to the bottom of the form and attach the pdf file under “external files”

-Scroll up and select “go”, then “proceed to check out”

If there is NOT a PDF quote attached for multiple compounds:

-On the Bearbuy homepage search for the item, make sure it matches the request exactly, and add to cart.

-If you can’t find the exact item, use the “non-catalog” form under the frequently used forms section.

-Enter in the supplier, product description, catalogue number and price. Try to be specific in the product description.

-Select commodity code 00025 Chemicals, and enter the relevant information for quantity. Select “No” for the Protected health drop down, and “Agree” for the conflict of interest question

-Scroll up and select “go”, then “proceed to check out”

=== Check out: ===

-Edit the procurement department and enter “333019”

-Edit the Accounting code and enter the corresponding Grant ID which should begin with PPSHOF

-Edit the Shipping address, select the appropriate address and name. You may have to look up the address by typing in “BH509” or “BH501”

-Finally, click “assign cart”, enter “Matthew Denny” and under notes write “Chemicals per attached quote John Smith March 2 Q125768” or leave blank for single items.

Quartzy and BearBuy

2020-08-04T21:50:41Z

Stefan:

Compounds are typically ordered by adding requests on quartzy.com. Once the request is approved, the order is placed on BearBuy (by the lab manager). Here are a few things to keep in mind.

= Placing requests and adding new vendors to BearBuy =

'''1)''' Whenever possible, if the lab still uses Quartzy, please enter (not place orders via Quartzy) your orders in Quartzy vs sending them directly to the lab manager (Henry). Entering it in Quartzy will help keep track of the whereabouts of the compounds you are ordering (qty, location, etc).
Henry will check Quartzy & place your orders.

'''2)''' If a vendor is not set up in BearBuy, have the vendor complete the *W-8BEN-E* form (for international vendors), or, the *W-8BEN* form (for domestic vendors). To check whether a vendor is setup in BearBuy, login via MyAccess and search through the suppliers.
The W8 forms are available from the purchasing manager Matthew Denny (matt.denny@ucsf.edu). Forward the completed form to Yvonne or Matt Denny so the vendor can be set up in BearBuy.

'''3)''' Please DO NOT place orders w/o PO #s, or, have vendors invoice UCSF w/o a PO #. An order, or, invoice w/o a PO # causes problems w/ purchasing & accounting. Don't place orders w/o PO #s. If you have an urgent order, you will still need a PO to place it. If necessary, consult Matt Denny (matt.denny@ucsf.edu) on how to best place/expedite urgent orders, or, if you have any questions about purchasing.

= Placing orders in BearBuy from Quartzy requests =

Written by Henry O'Donnell

=== How to place orders for the lab ===

- Log in to Quartzy and check for new order requests, take note of the total price, the supplier, name of the person who placed the order, and the grant ID

If there is a PDF quote attached for multiple compounds:

-Click on the order request and download the PDF, but rename the file by adding the requester’s name and the date. For Example, change “Q125768.pdf” to “John Smith March 2 Q125768.pdf”

-Copy the new file name (exclude .pdf), in this example you would copy “John Smith March 2 Q125768”

-Log in to MyAccess and open “BearBuy”, scroll down and select “Amount based PO”

-Input the name of the supplier (if the supplier is Tocris, input R&D)

-Under Product description write “Chemicals per attached quote John Smith March 2 Q125768”. Paste the name of the file to save time and avoid mistakes.

-Input the total price, select commodity code 00025 Chemicals, select “No” for the Protected health drop down, “No” for the services requested drop down, and “Agree” for the conflict of interest question

-Scroll to the bottom of the form and attach the pdf file under “external files”

-Scroll up and select “go”, then “proceed to check out”

If there is NOT a PDF quote attached for multiple compounds:

-On the Bearbuy homepage search for the item, make sure it matches the request exactly, and add to cart.

-If you can’t find the exact item, use the “non-catalog” form under the frequently used forms section.

-Enter in the supplier, product description, catalogue number and price. Try to be specific in the product description.

-Select commodity code 00025 Chemicals, and enter the relevant information for quantity. Select “No” for the Protected health drop down, and “Agree” for the conflict of interest question

-Scroll up and select “go”, then “proceed to check out”

=== Check out: ===

-Edit the procurement department and enter “333019”

-Edit the Accounting code and enter the corresponding Grant ID which should begin with PPSHOF

-Edit the Shipping address, select the appropriate address and name. You may have to look up the address by typing in “BH509” or “BH501”

-Finally, click “assign cart”, enter “Matthew Denny” and under notes write “Chemicals per attached quote John Smith March 2 Q125768” or leave blank for single items.

Quartzy and BearBuy

2020-08-04T21:29:19Z

Stefan:

Compounds are typically ordered by adding requests on quartzy.com. Once the request is approved, the order is placed on BearBuy (by the lab manager). Here are a few things to keep in mind.

= Placing requests and adding new vendors to BearBuy =

'''1)''' Whenever possible, if the lab still uses Quartzy, please enter (not place orders via Quartzy) your orders in Quartzy vs sending them directly to the lab manager (Henry). Entering it in Quartzy will help keep track of the whereabouts of the compounds you are ordering (qty, location, etc).
Henry will check Quartzy & place your orders.

'''2)''' If a vendor is not set up in BearBuy, have the vendor complete the W-8BEN-E form (for international vendors), or, the W-8BEN form (for domestic vendors). To check whether a vendor is setup in BearBuy, login via MyAccess and search through the suppliers.
The W8 forms are available from the purchasing manager Matthew Denny (matt.denny@ucsf.edu). Forward the completed form to Yvonne or Matt Denny so the vendor can be set up in BearBuy.

'''3)''' Please DO NOT place orders w/o PO #s, or, have vendors invoice UCSF w/o a PO #. An order, or, invoice w/o a PO # causes problems w/ purchasing & accounting. Don't place orders w/o PO #s. If you have an urgent order, you will still need a PO to place it. If necessary, consult Matt Denny (matt.denny@ucsf.edu) on how to best place/expedite urgent orders, or, if you have any questions about purchasing.

= Placing orders in BearBuy from Quartzy requests =

Written by Henry O'Donnell

=== How to place orders for the lab ===

- Log in to Quartzy and check for new order requests, take note of the total price, the supplier, name of the person who placed the order, and the grant ID

If there is a PDF quote attached for multiple compounds:

-Click on the order request and download the PDF, but rename the file by adding the requester’s name and the date. For Example, change “Q125768.pdf” to “John Smith March 2 Q125768.pdf”

-Copy the new file name (exclude .pdf), in this example you would copy “John Smith March 2 Q125768”

-Log in to MyAccess and open “BearBuy”, scroll down and select “Amount based PO”

-Input the name of the supplier (if the supplier is Tocris, input R&D)

-Under Product description write “Chemicals per attached quote John Smith March 2 Q125768”. Paste the name of the file to save time and avoid mistakes.

-Input the total price, select commodity code 00025 Chemicals, select “No” for the Protected health drop down, “No” for the services requested drop down, and “Agree” for the conflict of interest question

-Scroll to the bottom of the form and attach the pdf file under “external files”

-Scroll up and select “go”, then “proceed to check out”

If there is NOT a PDF quote attached for multiple compounds:

-On the Bearbuy homepage search for the item, make sure it matches the request exactly, and add to cart.

-If you can’t find the exact item, use the “non-catalog” form under the frequently used forms section.

-Enter in the supplier, product description, catalogue number and price. Try to be specific in the product description.

-Select commodity code 00025 Chemicals, and enter the relevant information for quantity. Select “No” for the Protected health drop down, and “Agree” for the conflict of interest question

-Scroll up and select “go”, then “proceed to check out”

=== Check out: ===

-Edit the procurement department and enter “333019”

-Edit the Accounting code and enter the corresponding Grant ID which should begin with PPSHOF

-Edit the Shipping address, select the appropriate address and name. You may have to look up the address by typing in “BH509” or “BH501”

-Finally, click “assign cart”, enter “Matthew Denny” and under notes write “Chemicals per attached quote John Smith March 2 Q125768” or leave blank for single items.

Quartzy and BearBuy

2020-08-04T21:19:07Z

Stefan:

Compounds are typically ordered by adding requests on quartzy.com. Once the request is approved, the order is placed on BearBuy (by the lab manager). Here are a few things to keep in mind.

= Adding new vendors to BearBuy =

'''1)''' Whenever possible, if the lab still uses Quartzy, please enter (not place orders via Quartzy) your orders in Quartzy vs sending them directly to the lab manager (Henry). Entering it in Quartzy will help keep track of the whereabouts of the compounds you are ordering (qty, location, etc).
Henry will check Quartzy & place your orders.

'''2)''' If a vendor is not set up in BearBuy, have the vendor complete the W-8BEN-E form (for international vendors), or, the W-8BEN form (for domestic vendors). To check whether a vendor is setup in BearBuy, login via MyAccess and search through the suppliers.
The W8 forms are available from the purchasing manager Matthew Denny (matt.denny@ucsf.edu). Forward the completed form to Yvonne or Matt Denny so the vendor can be set up in BearBuy.

'''3)''' Please DO NOT place orders w/o PO #s, or, have vendors invoice UCSF w/o a PO #. An order, or, invoice w/o a PO # causes problems w/ purchasing & accounting. Don't place orders w/o PO #s. If you have an urgent order, you will still need a PO to place it. If necessary, consult Matt Denny (matt.denny@ucsf.edu) on how to best place/expedite urgent orders, or, if you have any questions about purchasing.

= Placing orders in BearBuy from Quartzy requests =

Written by Henry O'Donnell

=== How to place orders for the lab ===

- Log in to Quartzy and check for new order requests, take note of the total price, the supplier, name of the person who placed the order, and the grant ID

If there is a PDF quote attached for multiple compounds:

-Click on the order request and download the PDF, but rename the file by adding the requester’s name and the date. For Example, change “Q125768.pdf” to “John Smith March 2 Q125768.pdf”

-Copy the new file name (exclude .pdf), in this example you would copy “John Smith March 2 Q125768”

-Log in to MyAccess and open “BearBuy”, scroll down and select “Amount based PO”

-Input the name of the supplier (if the supplier is Tocris, input R&D)

-Under Product description write “Chemicals per attached quote John Smith March 2 Q125768”. Paste the name of the file to save time and avoid mistakes.

-Input the total price, select commodity code 00025 Chemicals, select “No” for the Protected health drop down, “No” for the services requested drop down, and “Agree” for the conflict of interest question

-Scroll to the bottom of the form and attach the pdf file under “external files”

-Scroll up and select “go”, then “proceed to check out”

If there is NOT a PDF quote attached for multiple compounds:

-On the Bearbuy homepage search for the item, make sure it matches the request exactly, and add to cart.

-If you can’t find the exact item, use the “non-catalog” form under the frequently used forms section.

-Enter in the supplier, product description, catalogue number and price. Try to be specific in the product description.

-Select commodity code 00025 Chemicals, and enter the relevant information for quantity. Select “No” for the Protected health drop down, and “Agree” for the conflict of interest question

-Scroll up and select “go”, then “proceed to check out”

=== Check out: ===

-Edit the procurement department and enter “333019”

-Edit the Accounting code and enter the corresponding Grant ID which should begin with PPSHOF

-Edit the Shipping address, select the appropriate address and name. You may have to look up the address by typing in “BH509” or “BH501”

-Finally, click “assign cart”, enter “Matthew Denny” and under notes write “Chemicals per attached quote John Smith March 2 Q125768” or leave blank for single items.

Quartzy and BearBuy

2020-08-04T21:18:00Z

Stefan: Created page with "Compounds are typically ordered by adding requests on quartzy.com, once the request is approved, the order is placed on BearBuy (by the lab manager). Here are a few things to ..."

Compounds are typically ordered by adding requests on quartzy.com, once the request is approved, the order is placed on BearBuy (by the lab manager). Here are a few things to keep in mind.

= Adding new vendors to BearBuy =

'''1)''' Whenever possible, if the lab still uses Quartzy, please enter (not place orders via Quartzy) your orders in Quartzy vs sending them directly to the lab manager (Henry). Entering it in Quartzy will help keep track of the whereabouts of the compounds you are ordering (qty, location, etc).
Henry will check Quartzy & place your orders.

'''2)''' If a vendor is not set up in BearBuy, have the vendor complete the W-8BEN-E form (for international vendors), or, the W-8BEN form (for domestic vendors). To check whether a vendor is setup in BearBuy, login via MyAccess and search through the suppliers.
The W8 forms are available from the purchasing manager Matthew Denny (matt.denny@ucsf.edu). Forward the completed form to Yvonne or Matt Denny so the vendor can be set up in BearBuy.

'''3)''' Please DO NOT place orders w/o PO #s, or, have vendors invoice UCSF w/o a PO #. An order, or, invoice w/o a PO # causes problems w/ purchasing & accounting. Don't place orders w/o PO #s. If you have an urgent order, you will still need a PO to place it. If necessary, consult Matt Denny (matt.denny@ucsf.edu) on how to best place/expedite urgent orders, or, if you have any questions about purchasing.

= Placing orders in BearBuy from Quartzy requests =

Written by Henry O'Donnell

=== How to place orders for the lab ===

- Log in to Quartzy and check for new order requests, take note of the total price, the supplier, name of the person who placed the order, and the grant ID

If there is a PDF quote attached for multiple compounds:

-Click on the order request and download the PDF, but rename the file by adding the requester’s name and the date. For Example, change “Q125768.pdf” to “John Smith March 2 Q125768.pdf”

-Copy the new file name (exclude .pdf), in this example you would copy “John Smith March 2 Q125768”

-Log in to MyAccess and open “BearBuy”, scroll down and select “Amount based PO”

-Input the name of the supplier (if the supplier is Tocris, input R&D)

-Under Product description write “Chemicals per attached quote John Smith March 2 Q125768”. Paste the name of the file to save time and avoid mistakes.

-Input the total price, select commodity code 00025 Chemicals, select “No” for the Protected health drop down, “No” for the services requested drop down, and “Agree” for the conflict of interest question

-Scroll to the bottom of the form and attach the pdf file under “external files”

-Scroll up and select “go”, then “proceed to check out”

If there is NOT a PDF quote attached for multiple compounds:

-On the Bearbuy homepage search for the item, make sure it matches the request exactly, and add to cart.

-If you can’t find the exact item, use the “non-catalog” form under the frequently used forms section.

-Enter in the supplier, product description, catalogue number and price. Try to be specific in the product description.

-Select commodity code 00025 Chemicals, and enter the relevant information for quantity. Select “No” for the Protected health drop down, and “Agree” for the conflict of interest question

-Scroll up and select “go”, then “proceed to check out”

=== Check out: ===

-Edit the procurement department and enter “333019”

-Edit the Accounting code and enter the corresponding Grant ID which should begin with PPSHOF

-Edit the Shipping address, select the appropriate address and name. You may have to look up the address by typing in “BH509” or “BH501”

-Finally, click “assign cart”, enter “Matthew Denny” and under notes write “Chemicals per attached quote John Smith March 2 Q125768” or leave blank for single items.

Membrane Modeling

2019-11-18T21:18:45Z

Stefan:

Written by Stefan Gahbauer, 2019/11/03

In order to account for ligand desolvation and electrostatic interactions in the low-dielectric environment of the hydrophobic membrane core, a lipid-bilayer is generated around the target receptor and included in the docking score grid generation.
Aiming at a fast, robust and computationally effective equilibration of the lipid bilayer around the embedded transmembrane receptor, coarse-grained (CG) molecular dynamics (MD) simulations and (if needed) subsequent atomistic simulations are employed.

= Required software and datasets =

'''Gromacs''' (v5 or newer) - Molecular Dynamics software package (http://manual.gromacs.org/)

'''CHARMM36m force field''' (http://mackerell.umaryland.edu/charmm_ff.shtml)

'''MARTINI''' Coarse-grained force field parameters(http://cgmartini.nl/)

'''DSSP''' - Secondary Structure assignment (https://swift.cmbi.umcn.nl/gv/dssp/ , https://anaconda.org/salilab/dssp)

'''martinize.py''' - Coarse-graining atomistic protein structures (http://cgmartini.nl/index.php/tools2/proteins-and-bilayers)

'''insane.py''' - INSerting proteins in coarse-grained MembrANE (http://cgmartini.nl/index.php/tools2/proteins-and-bilayers)

'''initram.sh''' and '''backward.py''' - Conversion of coarse-grained system to atomistic resolution (http://cgmartini.nl/index.php/tools2/resolution-transformation)

= 1) Setting up the coarse-grained system =

This is automated in the script:

/mnt/nfs/home/stefan/zzz.scripts/INSERT-MEMBRANE/FILES/0001-prepare-protein-CG-membrane.sh

== 1.1) Prepare your files ==

Copy the script above to your working directory.

Copy your rec.pdb to your working directory.

If your rec.pdb has gaps, e.g. unresolved loops between transmembrane helices in case of GPCRs, try to model missing residues.

One way is to use MODELLER following https://salilab.org/modeller/wiki/Missing%20residues.

Corresponding input scripts for modeller can be found in:

/mnt/nfs/home/stefan/zzz.scripts/INSERT-MEMBRANE/FILES/modeller

== 1.2) Run the script ==

Login to gimel2.

./0001-prepare-protein-CG-membrane.sh

The script reads rec.pdb and copies all other required files from

/mnt/nfs/home/stefan/zzz.scripts/INSERT-MEMBRANE/FILES/gromacs

=== Workflow ===

'''a.''' Generate CHARMM36m force field parameters of your protein in a Gromacs-readable format.

Used tool: gmx pdb2gmx

Output files are stored in the generated ''pdb2gmx'' directory

-conf.gro / conf.pdb - Gromacs coordinate file

-topol.top / Protein-atomistic.itp - Gromacs topology file, i.e. force field description of your input structure

-posre.itp - Position restraints for heavy atoms of atomistic protein strucutre.

'''b.''' Build coarse-grained structure

Used tool: martinize.py

Output files are stored in the generated ''martini'' directory.

-chain_.ssd - Output from the DSSP program that is called by martinize.py

-prot-cg.pdb - Coarse-grained protein structure

-prot-cg.top - Coarse-grained Martini topology of system

-Protein.itp - Coarse-grained Martini description of Protein structure

-prot-rot.pdb - Coarse-grained protein structure aligned along z-axis of the simulation box according to the proteins first principal component axis. This ensures the correct placement of the protein during membrane preparation. '''You may have to adjust the orientation of your input structure prior to membrane modeling.'''

'''c.''' Build coarse-grained membrane

Used tool: insane.py

Here, a lipid bilayer will be created around the protein structure (in the x/y-plane) and water will be added to the system. The default box shape is rectangular and the size is set to x,y=10nm, z=11nm. This can be changed in the ./insane.py command line. The default lipid type is POPC, you can change that to arbitrary lipid compositions using the -l and -u options of of insane.py.

Output files are stored in the ''martini'' directory.

-out.top / topol-cg.top - Topology of coarse-grained system

-cg-membrane.gro/.pdb - Coarse-grained system coordinates. '''Carefully inspect and visualize the cg-membrane.pdb.'''

Use PyMOL to check if you're protein is embedded correctly in the lipid bilayer.

= 2) Simulating the coarse-grained system =

This is automated in the script:

/mnt/nfs/home/stefan/zzz.scripts/INSERT-MEMBRANE/FILES/0002-run-CG-Minimization-and-MD.sh

== 2.1) Run the script ==

Copy the script above to your working directory.

./0002-run-CG-Minimization-and-MD.sh

=== Workflow ===

'''a.''' Minimize coarse-grained system

Used tools: gmx grompp , gmx mdrun

gmx grompp generates a single .tpr file that contains all information necessary for running a MD simulation or minimization using gmx mdrun.

Minimization parameters are provided in martini_new-rf_min.mdp. The system will be minimized in 500 steps using steepest descent. The protein structure will be frozen during minimization.

Output files are stored in the ''martini'' directory.

-min.tpr - MD run input file

-min.log - Output log file from minimization

-min.trr - Minimization trajectory

-min.gro - Minimized system coordinates

'''b.''' Simulate coarse-grained system

MD simulation parameters are provided in martini_v2.x_new-rf.mdp. Strong position restraints are applied on the protein structure during the simulation. The system will be simulated for 50ns.

Output files are stored in the ''martini'' directory.

-md.tpr - MD run input file

-md.log - Output log file from simulation

-md.trr - lossless trajectory of simulation

-md.xtc - coordinates of simulation trajectory

-md.gro - coordinates of final simulation snapshot

'''The simulation will run for roughly 3 hours.'''

= 3) Converting coarse-grained system to atomistic resolution and select lipid atoms for grid generation =

This is automated in the script:

/mnt/nfs/home/stefan/zzz.scripts/INSERT-MEMBRANE/FILES/0003-backmap-and-lpd-selection.sh

== 3.1) Run the script ==

Copy the script above to your working directory.

./0003-backmap-and-lpd-selection.sh

=== Workflow ===

'''a.''' Backmapping from coarse-grained to atomistic

Used tool: gmx trjconv, initram.sh

gmx trjconv can perform a variety of conversions of MD trajectory, e.g. making molecules broken over the periodic boundary conditions whole again.

initram.sh calls the backward.py program which performs the backmapping of input coarse-grained to atomistic systems, and performs a small series of short minimizations and simulations to relax the backmapped system.

Output files are stored in the generated ''backmap'' directory.

-0-backmapped.gro / projected.gro - initial backmapped coordinates

-backmapped.top - Topology of atomistic system

-1-EM*/2-EM* - Output from minimizations

-3-mdpr*/4-mdpr*/5-mdpr*/6-mdpr* - Output from simulations

-backmapped.gro - Coordinates of final backmapped and relaxed system

'''This may need a few attempts to work all the way through. There is a while-loop that only stops until all relaxation steps have finished.'''

'''b.''' Replacing backmapped protein with initial atomistic protein structure

Used tool: PyMOL script align.pml

The pymol script will align the initial "Gromacs"-protein structure (conf.pdb) onto the backmapped structure and combine the fitted protein coordinates with the coordinates of the lipid and solvent environment.

Output files are stored in the generated ''backmap/prepare_AA_system'' directory.

-conf-fitted.pdb - Fitted initial protein structure

-backmapped-environment.pdb - All membrane and water coordinates

-fitted_system.pdb - Complete system containing fitted protein and environment coordinates

'''Be sure that fitted_system.pdb has the same number of coordinates as backmapped-mol.pdb.''' If there is a discrepancy there might be an issue with the PyMOL version you're using to run align.pml. Using PyMOL v2 or newer seems to avoid any issues. You can also generate backmapped-environment.pdb manually by taking all POPC and Water cooridnates from backmapped-mol.pdb.

'''c.''' Run minimizations of atomistic system

Used tools: gmx grompp, gmx mdrun

Output files are stored in the ''backmap/prepare_AA_system'' directory.

Tow minimizations will be calculated.

1) Minimization with frozen protein coordinates: 1,500 steps steepest descent (min_freeze.mdp).

-min_freeze* - Output files of first minimization

2) Minimization of full system: 500 steps (min.mdp).

-min* - Output files of second minimization

'''d.''' Select lipid atoms for DOCK grid generation

Used tools: PyMOL script prepare.pml

This will select carbon and hydrogen atoms of the hydrophobic lipid tail segments in a radius of 1.7 nm around the protein and assign them to the atom type "LPD"

You need to provide the rec.pdb to want to use for docking (potentially with missing loops) at that step as xtal-prot.pdb

Output files are stored in the generated ''backmap/prepare_AA_system/prepare_min'' directory.

-shell-LPD.pdb - all LPD atoms selected for grid generation

Add these coordinates to your docking protein structure and provide a amb.crg.oxt file adding

C lpd 0.000 LIPID SPHERE

Now you can run blastermaster.

Membrane Modeling

2019-11-03T00:28:29Z

Stefan: Created page with "Written by Stefan Gahbauer, 2019/11/03 In order to account for ligand desolvation and electrostatic interactions in the low-dielectric environment of the hydrophobic membrane..."

Written by Stefan Gahbauer, 2019/11/03

In order to account for ligand desolvation and electrostatic interactions in the low-dielectric environment of the hydrophobic membrane core, a lipid-bilayer is generated around the target receptor and included in the docking score grid generation.
Aiming at a fast, robust and computationally effective equilibration of the lipid bilayer around the embedded transmembrane receptor, coarse-grained (CG) molecular dynamics (MD) simulations and (if needed) subsequent atomistic simulations are employed.

= Required software and datasets =

'''Gromacs''' (v5 or newer) - Molecular Dynamics software package (http://manual.gromacs.org/)

'''CHARMM36m force field''' (http://mackerell.umaryland.edu/charmm_ff.shtml)

'''MARTINI''' Coarse-grained force field parameters(http://cgmartini.nl/)

'''DSSP''' - Secondary Structure assignment (https://swift.cmbi.umcn.nl/gv/dssp/ , https://anaconda.org/salilab/dssp)

'''martinize.py''' - Coarse-graining atomistic protein structures (http://cgmartini.nl/index.php/tools2/proteins-and-bilayers)

'''insane.py''' - INSerting proteins in coarse-grained MembrANE (http://cgmartini.nl/index.php/tools2/proteins-and-bilayers)

'''initram.sh''' and '''backward.py''' - Conversion of coarse-grained system to atomistic resolution (http://cgmartini.nl/index.php/tools2/resolution-transformation)

= 1) Setting up the coarse-grained system =

This is automated in the script:

/mnt/nfs/home/stefan/zzz.scripts/INSERT-MEMBRANE/FILES/0001-prepare-protein-CG-membrane.sh

== 1.1) Prepare your files ==

Copy the script above to your working directory.

Copy your rec.pdb to your working directory.

If your rec.pdb has gaps, e.g. unresolved loops between transmembrane helices in case of GPCRs, try to model missing residues.

One way is to use MODELLER following https://salilab.org/modeller/wiki/Missing%20residues.

Corresponding input scripts for modeller can be found in:

/mnt/nfs/home/stefan/zzz.scripts/INSERT-MEMBRANE/FILES/modeller

== 1.2) Run the script ==

Login to gimel2.

./0001-prepare-protein-CG-membrane.sh

The script reads rec.pdb and copies all other required files from

/mnt/nfs/home/stefan/zzz.scripts/INSERT-MEMBRANE/FILES/gromacs

=== Workflow ===

'''a.''' Generate CHARMM36m force field parameters of your protein in a Gromacs-readable format.

Used tool: gmx pdb2gmx

Output files are stored in the generated ''pdb2gmx'' directory

-conf.gro / conf.pdb - Gromacs coordinate file

-topol.top / Protein-atomistic.itp - Gromacs topology file, i.e. force field description of your input structure

-posre.itp - Position restraints for heavy atoms of atomistic protein strucutre.

'''b.''' Build coarse-grained structure

Used tool: martinize.py

Output files are stored in the generated ''martini'' directory.

-chain_.ssd - Output from the DSSP program that is called by martinize.py

-prot-cg.pdb - Coarse-grained protein structure

-prot-cg.top - Coarse-grained Martini topology of system

-Protein.itp - Coarse-grained Martini description of Protein structure

-prot-rot.pdb - Coarse-grained protein structure aligned along z-axis of the simulation box according to the proteins first principal component axis. This ensures the correct placement of the protein during membrane preparation. '''You may have to adjust the orientation of your input structure prior to membrane modeling.'''

'''c.''' Build coarse-grained membrane

Used tool: insane.py

Here, a lipid bilayer will be created around the protein structure (in the x/y-plane) and water will be added to the system. The default box shape is rectangular and the size is set to x,y=10nm, z=11nm. This can be changed in the ./insane.py command line. The default lipid type is POPC, you can change that to arbitrary lipid compositions using the -l and -u options of of insane.py.

Output files are stored in the ''martini'' directory.

-out.top / topol-cg.top - Topology of coarse-grained system

-cg-membrane.gro - Coarse-grained system coordinates. '''Carefully inspect and visualize the cg-membrane.gro.'''

Use PyMOL to check if you're protein is embedded correctly in the lipid bilayer.

= 2) Simulating the coarse-grained system =

This is automated in the script:

/mnt/nfs/home/stefan/zzz.scripts/INSERT-MEMBRANE/FILES/0002-run-CG-Minimization-and-MD.sh

== 2.1) Run the script ==

Copy the script above to your working directory.

./0002-run-CG-Minimization-and-MD.sh

=== Workflow ===

'''a.''' Minimize coarse-grained system

Used tools: gmx grompp , gmx mdrun

gmx grompp generates a single .tpr file that contains all information necessary for running a MD simulation or minimization using gmx mdrun.

Minimization parameters are provided in martini_new-rf_min.mdp. The system will be minimized in 500 steps using steepest descent. The protein structure will be frozen during minimization.

Output files are stored in the ''martini'' directory.

-min.tpr - MD run input file

-min.log - Output log file from minimization

-min.trr - Minimization trajectory

-min.gro - Minimized system coordinates

'''b.''' Simulate coarse-grained system

MD simulation parameters are provided in martini_v2.x_new-rf.mdp. Strong position restraints are applied on the protein structure during the simulation. The system will be simulated for 50ns.

Output files are stored in the ''martini'' directory.

-md.tpr - MD run input file

-md.log - Output log file from simulation

-md.trr - lossless trajectory of simulation

-md.xtc - coordinates of simulation trajectory

-md.gro - coordinates of final simulation snapshot

'''The simulation will run for roughly 3 hours.'''

= 3) Converting coarse-grained system to atomistic resolution and select lipid atoms for grid generation =

This is automated in the script:

/mnt/nfs/home/stefan/zzz.scripts/INSERT-MEMBRANE/FILES/0003-backmap-and-lpd-selection.sh

== 3.1) Run the script ==

Copy the script above to your working directory.

./0003-backmap-and-lpd-selection.sh

=== Workflow ===

'''a.''' Backmapping from coarse-grained to atomistic

Used tool: gmx trjconv, initram.sh

gmx trjconv can perform a variety of conversions of MD trajectory, e.g. making molecules broken over the periodic boundary conditions whole again.

initram.sh calls the backward.py program which performs the backmapping of input coarse-grained to atomistic systems, and performs a small series of short minimizations and simulations to relax the backmapped system.

Output files are stored in the generated ''backmap'' directory.

-0-backmapped.gro / projected.gro - initial backmapped coordinates

-backmapped.top - Topology of atomistic system

-1-EM*/2-EM* - Output from minimizations

-3-mdpr*/4-mdpr*/5-mdpr*/6-mdpr* - Output from simulations

-backmapped.gro - Coordinates of final backmapped and relaxed system

'''This may need a few attempts to work all the way through. There is a while-loop that only stops until all relaxation steps have finished.'''

'''b.''' Replacing backmapped protein with initial atomistic protein structure

Used tool: PyMOL script align.pml

The pymol script will align the initial "Gromacs"-protein structure (conf.pdb) onto the backmapped structure and combine the fitted protein coordinates with the coordinates of the lipid and solvent environment.

Output files are stored in the generated ''backmap/prepare_AA_system'' directory.

-conf-fitted.pdb - Fitted initial protein structure

-backmapped-environment.pdb - All membrane and water coordinates

-fitted_system.pdb - Complete system containing fitted protein and environment coordinates

'''Be sure that fitted_system.pdb has the same number of coordinates as backmapped-mol.pdb.''' If there is a discrepancy there might be an issue with the PyMOL version you're using to run align.pml. Using PyMOL v2 or newer seems to avoid any issues. You can also generate backmapped-environment.pdb manually by taking all POPC and Water cooridnates from backmapped-mol.pdb.

'''c.''' Run minimizations of atomistic system

Used tools: gmx grompp, gmx mdrun

Output files are stored in the ''backmap/prepare_AA_system'' directory.

Tow minimizations will be calculated.

1) Minimization with frozen protein coordinates: 1,500 steps steepest descent (min_freeze.mdp).

-min_freeze* - Output files of first minimization

2) Minimization of full system: 500 steps (min.mdp).

-min* - Output files of second minimization

'''d.''' Select lipid atoms for DOCK grid generation

Used tools: PyMOL script prepare.pml

This will select carbon and hydrogen atoms of the hydrophobic lipid tail segments in a radius of 1.7 nm around the protein and assign them to the atom type "LPD"

You need to provide the rec.pdb to want to use for docking (potentially with missing loops) at that step as xtal-prot.pdb

Output files are stored in the generated ''backmap/prepare_AA_system/prepare_min'' directory.

-shell-LPD.pdb - all LPD atoms selected for grid generation

Add these coordinates to your docking protein structure and provide a amb.crg.oxt file adding

C lpd 0.000 LIPID SPHERE

Now you can run blastermaster.