Scoreopt: Difference between revisions
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==If You Have Problems== | |||
If you do not have an eel1 file | |||
If you do not have an eel1 file or things are not running smoothly with your pdb file here are two options of how to get around it. | |||
An eel1 file can be automatically created for you with this script: | An eel1 file can be automatically created for you with this script: | ||
| Line 22: | Line 23: | ||
$mud/to_eel1.csh your.pdb (see http://wiki.bkslab.org/index.php/Analysing_the_results for further directions) | $mud/to_eel1.csh your.pdb (see http://wiki.bkslab.org/index.php/Analysing_the_results for further directions) | ||
If you have special molecules the other | If you have special molecules the other way to approch this problem is to: | ||
a) read your pdb into chimera | a) read your pdb into chimera | ||
b) add hydrogens in chimera ('Tools_>Structure Editing->AddH' show labels at that time 'Actions->Lable->IDATM type' and make sure you are happy with the molecule) | b) add hydrogens in chimera ('Tools_>Structure Editing->AddH' show labels at that time 'Actions->Lable->IDATM type' and make sure you are happy with the molecule) | ||
c) charge the molecule in chimera ('Tools->Structure Editing-> AddCharge') | c) charge the molecule in chimera ('Tools->Structure Editing-> AddCharge') | ||
d) write out the molecule out as a filename.mol2 | d) write out the molecule out as a filename.mol2 | ||
e) run the scoreopt script from above | |||
----- | |||
If things are still not working just see the header of the .mol2 file and make sure that the header is in the correct format (there should only be 5 lines between @<TRIPOS>MOLECULE and @<TRIPOS>ATOM, and the new to_eel1.mol2 created in line two should have a new label in the format of four letters and eight numbers ie. AAAA12345678.) | |||
WRONG Header !!!!! | |||
---------------- | |||
@<TRIPOS>MOLECULE | |||
obj16.pdb | |||
15 15 1 0 0 | |||
SMALL | |||
NO_CHARGES | |||
@<TRIPOS>ATOM | |||
---------------- | |||
RIGHT Header !!!! | |||
---------------- | |||
@<TRIPOS>MOLECULE | |||
TEMP12345678 | |||
24 24 0 0 0 | |||
SMALL | |||
USER_CHARGES | |||
@<TRIPOS>ATOM | |||
---------------- | |||
Revision as of 19:46, 8 February 2012
Overview
Scoreopt allows you to rescore poses after a docking run is complete
Usage
Before using scoreopt, you should have a pdb (or eel1 or mol2) file with the poses to be rescored.
$mud/doscoreopt.csh <filename.eel1> <path to grids>
Output is combine.rescores ( in the form of combine.scores )
<id> <shape> <elect> <VdW> <polar solv> <apolar solv> <total> <subdir>
If You Have Problems
If you do not have an eel1 file or things are not running smoothly with your pdb file here are two options of how to get around it.
An eel1 file can be automatically created for you with this script:
$mud/to_eel1.csh your.pdb (see http://wiki.bkslab.org/index.php/Analysing_the_results for further directions)
If you have special molecules the other way to approch this problem is to:
a) read your pdb into chimera
b) add hydrogens in chimera ('Tools_>Structure Editing->AddH' show labels at that time 'Actions->Lable->IDATM type' and make sure you are happy with the molecule)
c) charge the molecule in chimera ('Tools->Structure Editing-> AddCharge')
d) write out the molecule out as a filename.mol2
e) run the scoreopt script from above
If things are still not working just see the header of the .mol2 file and make sure that the header is in the correct format (there should only be 5 lines between @<TRIPOS>MOLECULE and @<TRIPOS>ATOM, and the new to_eel1.mol2 created in line two should have a new label in the format of four letters and eight numbers ie. AAAA12345678.)
WRONG Header !!!!!
@<TRIPOS>MOLECULE
obj16.pdb
15 15 1 0 0
SMALL
NO_CHARGES
@<TRIPOS>ATOM
RIGHT Header !!!!
@<TRIPOS>MOLECULE
TEMP12345678
24 24 0 0 0
SMALL
USER_CHARGES
@<TRIPOS>ATOM