Membrane Modeling - Revision history

Iamkaant at 21:36, 31 May 2023

2023-05-31T21:36:51Z

← Older revision		Revision as of 21:36, 31 May 2023
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	''If the mentioned problem occurs, import the last coordinates of the run (*-out.cms) into Maestro, open Minimization menu, load the structure from the workspace, and apply restraints on lipid and protein (force restraint of 10 is usually enough). Then run a minimization for 100 ps, and try to run NgPT MD starting from the optimized structure.''		''If the mentioned problem occurs, import the last coordinates of the run (*-out.cms) into Maestro, open Minimization menu, load the structure from the workspace, and apply restraints on lipid and protein (force restraint of 10 is usually enough). Then run a minimization for 100 ps, and try to run NgPT MD starting from the optimized structure.''

	'' NPT ensemble can safely be used instead of NgPT''		''''' NPT ensemble can safely be used instead of NgPT'''''

	Copy the project folder (desmond_md_job_X) to gimel, login to <u>gimel5</u>, edit desmond_md_job_X.sh: delete <code>-lic DESMOND_GPGPU:16</code> and insert <code>-HOST gimel5.gpu</code> (or <code>gimel5.heavygpu</code>). Export <code>$SCHRODINGER</code> variable:		Copy the project folder (desmond_md_job_X) to gimel, login to <u>gimel5</u>, edit desmond_md_job_X.sh: delete <code>-lic DESMOND_GPGPU:16</code> and insert <code>-HOST gimel5.gpu</code> (or <code>gimel5.heavygpu</code>). Export <code>$SCHRODINGER</code> variable:

Iamkaant at 21:27, 31 May 2023

2023-05-31T21:27:25Z

← Older revision		Revision as of 21:27, 31 May 2023
Line 263:		Line 263:
	''If the mentioned problem occurs, import the last coordinates of the run (*-out.cms) into Maestro, open Minimization menu, load the structure from the workspace, and apply restraints on lipid and protein (force restraint of 10 is usually enough). Then run a minimization for 100 ps, and try to run NgPT MD starting from the optimized structure.''		''If the mentioned problem occurs, import the last coordinates of the run (*-out.cms) into Maestro, open Minimization menu, load the structure from the workspace, and apply restraints on lipid and protein (force restraint of 10 is usually enough). Then run a minimization for 100 ps, and try to run NgPT MD starting from the optimized structure.''

	''~~'''TO CHECK''':~~ NPT ensemble.''		'' NPT ensemble can safely be used instead of NgPT''

	Copy the project folder (desmond_md_job_X) to gimel, login to <u>gimel5</u>, edit desmond_md_job_X.sh: delete <code>-lic DESMOND_GPGPU:16</code> and insert <code>-HOST gimel5.gpu</code> (or <code>gimel5.heavygpu</code>). Export <code>$SCHRODINGER</code> variable:		Copy the project folder (desmond_md_job_X) to gimel, login to <u>gimel5</u>, edit desmond_md_job_X.sh: delete <code>-lic DESMOND_GPGPU:16</code> and insert <code>-HOST gimel5.gpu</code> (or <code>gimel5.heavygpu</code>). Export <code>$SCHRODINGER</code> variable:

Iamkaant at 17:59, 10 January 2023

2023-01-10T17:59:57Z

← Older revision		Revision as of 17:59, 10 January 2023
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	Use <code>datasub1</code> file to extract residue numbers for the membrane placement in Maestro.		Use <code>datasub1</code> file to extract residue numbers for the membrane placement in Maestro.
	See ppm3_instructions.docx file in the program directory for more detail. ~~Test~~		See ppm3_instructions.docx file in the program directory for more detail.

Iamkaant at 17:59, 10 January 2023

2023-01-10T17:59:39Z

← Older revision		Revision as of 17:59, 10 January 2023
Line 552:		Line 552:

	Use <code>datasub1</code> file to extract residue numbers for the membrane placement in Maestro.		Use <code>datasub1</code> file to extract residue numbers for the membrane placement in Maestro.
	See ppm3_instructions.docx file in the program directory for more detail.		See ppm3_instructions.docx file in the program directory for more detail. Test

Iamkaant: added the note to export $SCHRODINGER variable before running the script

2022-10-31T22:58:41Z

added the note to export $SCHRODINGER variable before running the script

← Older revision		Revision as of 22:58, 31 October 2022
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	'''''TO CHECK''': NPT ensemble.''		'''''TO CHECK''': NPT ensemble.''

	Copy the project folder (desmond_md_job_X) to gimel, login to <u>gimel5</u>, edit desmond_md_job_X.sh: delete <code>-lic DESMOND_GPGPU:16</code> and insert <code>-HOST gimel5.gpu</code> (or <code>gimel5.heavygpu</code>). Run .sh file, and your task will be submitted to a queue. For my system it took 1.5 hr to complete.		Copy the project folder (desmond_md_job_X) to gimel, login to <u>gimel5</u>, edit desmond_md_job_X.sh: delete <code>-lic DESMOND_GPGPU:16</code> and insert <code>-HOST gimel5.gpu</code> (or <code>gimel5.heavygpu</code>). Export <code>$SCHRODINGER</code> variable:

			<code>SCHRODINGER=/nfs/soft2/schrodinger/2023-3/</code> (or a newer version)

			Run .sh file, and your task will be submitted to a queue. For my system it took 1.5 hr to complete.

	Download the project folder to your PC, open Maestro, click <code>Import structure</code> and open <code>-out.cms</code>, click on <code>T</code> icon at the new entry in project table and click <code>Display Trajectory Snapshots</code>. Select the last one, click <code>Display</code> and check if the protein did not change position during MD run, then click <code>Export</code>, to Project Table, Frames Selected only. You will get a new entry in the Project Table. Export it to a <code>.pdb</code> file.		Download the project folder to your PC, open Maestro, click <code>Import structure</code> and open <code>-out.cms</code>, click on <code>T</code> icon at the new entry in project table and click <code>Display Trajectory Snapshots</code>. Select the last one, click <code>Display</code> and check if the protein did not change position during MD run, then click <code>Export</code>, to Project Table, Frames Selected only. You will get a new entry in the Project Table. Export it to a <code>.pdb</code> file.

Iamkaant at 21:20, 4 September 2022

2022-09-04T21:20:11Z

← Older revision		Revision as of 21:20, 4 September 2022
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	<code>~ak87/exa/PROGRAM/OPM-MEMBRANE/immers<1membrane.inp>rec-opm.out</code>		<code>~ak87/exa/PROGRAM/OPM-MEMBRANE/immers<1membrane.inp>rec-opm.out</code>

	Use <code>datasub1</code> file to extract residue numbers for the membrane placement in Maestro		Use <code>datasub1</code> file to extract residue numbers for the membrane placement in Maestro.
			See ppm3_instructions.docx file in the program directory for more detail.

Iamkaant: added the manual for membrane positioning

2022-09-04T21:19:22Z

added the manual for membrane positioning

← Older revision		Revision as of 21:19, 4 September 2022
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	save shell-LPD.pdb, shell		save shell-LPD.pdb, shell
	</syntaxhighlight>		</syntaxhighlight>

			== Positioning of the membrane ==
			If there is no precomputed membrane position from OPM or MemProtMD, you can model it using PPM 3.0 webserver (https://opm.phar.umich.edu/ppm_server3) or standalone software. The software is installed in <code>/nfs/home/ak87/exa/PROGRAM/OPM-MEMBRANE</code>. Copy <code>res.lib</code> file from the program directory to the directory with your .pdb file. Create input file like this:<syntaxhighlight lang="shell">
			1
			0 PMm out rec.pdb
			</syntaxhighlight><blockquote>0 or 1 -“do not use” or “use” heteroatoms in the input PDB file, respectively (solvent molecules are always excluded).

			MOM - type of membrane (see list of 3-letter codes for membranes below)

			“in” or “out” means topology of N-terminus of first subunit included in the corresponding input PDB file

			With this option, for every input pdb file, the program will selected automatically the flat or curved membrane boundaries, whichever had the lower calculated transfer energy.</blockquote>Then run the program:

			<code>~ak87/exa/PROGRAM/OPM-MEMBRANE/immers<1membrane.inp>rec-opm.out</code>

			Use <code>datasub1</code> file to extract residue numbers for the membrane placement in Maestro

Iamkaant: added troubleshooting of MD runs

2022-06-14T02:51:31Z

added troubleshooting of MD runs

← Older revision		Revision as of 02:51, 14 June 2022
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	Then use <u>Molecular Dynamics</u> menu to set up the calculation. Select prepared system, click <code>Load</code> on top of the menu. Put simulation time of 5 ns, <code>Advanced Options</code> -- <code>Restraints</code> -- <code>Add.</code> Select protein, and put <code>Force Constant</code> of 100, click <code>Apply</code> and <code>OK.</code> Then click down arrow left of the <code>Run</code> button in the parent window and click <code>Write</code>.		Then use <u>Molecular Dynamics</u> menu to set up the calculation. Select prepared system, click <code>Load</code> on top of the menu. Put simulation time of 5 ns, <code>Advanced Options</code> -- <code>Restraints</code> -- <code>Add.</code> Select protein, and put <code>Force Constant</code> of 100, click <code>Apply</code> and <code>OK.</code> Then click down arrow left of the <code>Run</code> button in the parent window and click <code>Write</code>.

			'''''NOTE''': In my experience, restrained MD runs with NgPT in Schrodinger often fail with the following message:''

			<code>''Allowed momentum exceeded on 17 particles.''</code>

			''This seems to be related to the interference of restraints and the ensemble, as no such error is observed if no restraints are imposed, or if NVT ensemble is used. Still, NgPT ensemble is important for correct membrane sampling, because simulations at NVT long enough to permit membrane relaxation, lead to the smearing of the lipid bilayer and the formation of empty space.''

			''If the mentioned problem occurs, import the last coordinates of the run (*-out.cms) into Maestro, open Minimization menu, load the structure from the workspace, and apply restraints on lipid and protein (force restraint of 10 is usually enough). Then run a minimization for 100 ps, and try to run NgPT MD starting from the optimized structure.''

			'''''TO CHECK''': NPT ensemble.''

	Copy the project folder (desmond_md_job_X) to gimel, login to <u>gimel5</u>, edit desmond_md_job_X.sh: delete <code>-lic DESMOND_GPGPU:16</code> and insert <code>-HOST gimel5.gpu</code> (or <code>gimel5.heavygpu</code>). Run .sh file, and your task will be submitted to a queue. For my system it took 1.5 hr to complete.		Copy the project folder (desmond_md_job_X) to gimel, login to <u>gimel5</u>, edit desmond_md_job_X.sh: delete <code>-lic DESMOND_GPGPU:16</code> and insert <code>-HOST gimel5.gpu</code> (or <code>gimel5.heavygpu</code>). Run .sh file, and your task will be submitted to a queue. For my system it took 1.5 hr to complete.

Iamkaant: changed Pymol script: Hs are not removed from lipids

2022-04-26T06:53:58Z

changed Pymol script: Hs are not removed from lipids

← Older revision		Revision as of 06:53, 26 April 2022
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	create MEM, ////POPC		create MEM, ////POPC

	remove /MEM////HS		# these atom numbers do not exist in POPC or DPPC
	remove /MEM////HX		# therefore, we do not remove protons from the lipid
	remove /MEM////HY		# structure to make more spheres. Uncomment these
	remove /MEM////H*B		# lines and change to proper H numbers if needed.
	remove /MEM////H*A		#remove /MEM////HS
	remove /MEM////H*C		#remove /MEM////HX
			#remove /MEM////HY
			#remove /MEM////H*B
			#remove /MEM////H*A
			#remove /MEM////H*C

	remove /MEM////C1		remove /MEM////C1

Iamkaant: added protocol for MemProtMD

2022-04-21T01:42:06Z

added protocol for MemProtMD

@@ Line 468: / Line 468: @@
 cp ligand.desolv.heavy ../dockfiles/.
 echo "DONE!"
 </syntaxhighlight>