Hello,
I would like to minimise the binding site including ligands, cofactors and water molecules.
I have the following script:
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runCommand("open " + pdbpath + pdbid + "_chimera.pdb")
runCommand("findclash 'ligand | solvent' test '~ligand | ~solvent' overlapCutoff -1.0 hbondAllowance 0.0 intraMol false selectClashes true")
runCommand("sel up")
runCommand("namesel tomin")
runCommand("minimize spec tomin fragment true cache true prep true freeze :@ca cgsteps 0")
runCommand("write format pdb #0 " + pdbpath + pdbid + "_min.pdb")
runCommand("write format mol2 #0 " + pdbpath + pdbid + "_min.mol2")
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I am facing two issues:
1) Water molecules are deleted by prep. Is there as way of preventing this.
I have tried creating a custom preferences file like:
echo "{'AddCharge': {'charge method': 'Gasteiger'}," > ${DIR}/chimera_preferences
#echo " 'DockPrep': {'delete solvent': 'false'}," > ${DIR}/chimera_preferences
echo " 'DockPrep': {'incomplete side chains': 'rotamers'}}" >> ${DIR}/chimera_preferences
However, the second option is not recognised. Does it exist and, if so, what would be the correct syntax?
2) The second problem is that the selection is ignored and every atom except CAs is minimised.
Another option I have tried be setting prep to false and running it beforehand:
models = chimera.openModels.open(pdbpath + pdbid + "_chimera.pdb")
prep(models, delSolvent=False)
But, again, if I do this, the selection is also ignored.
Best,
Miro
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Edelmiro Moman, PhD
South Ural State University - SUSU