Sample Additional Ring Puckers - Revision history

TBalius at 17:12, 20 July 2018

2018-07-20T17:12:48Z

← Older revision		Revision as of 17:12, 20 July 2018
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	The smiles file contain one smiles. It should have all stereo chemistry defined and be in the right protonation and tautomerazation state.		The smiles file contain one smiles. It should have all stereo chemistry defined and be in the right protonation and tautomerazation state.

	Here is a wrapper script to run this on a smiles file that contains multiple smiles.		Here is a wrapper script (named wrapper_build_ligand_tautprot_smiles_cov.csh) to run this on a smiles file that contains multiple smiles.

	#set mountdir = `pwd`		#set mountdir = `pwd`

TBalius at 16:14, 20 July 2018

2018-07-20T16:14:51Z

← Older revision		Revision as of 16:14, 20 July 2018
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	$DOCKBASE/ligand/generate/build_ligand_tautprot_smiles_covalent.sh smi_file.smi		$DOCKBASE/ligand/generate/build_ligand_tautprot_smiles_covalent.sh smi_file.smi

	The smiles file contain one smiles. It should ~~should be~~ have all stereo chemistry defined and be in the right protonation and tautomerazation ~~states~~.		The smiles file contain one smiles. It should have all stereo chemistry defined and be in the right protonation and tautomerazation state.

	~~here~~ is a wrapper script to run this on a smiles file that contains multiple smiles.		Here is a wrapper script to run this on a smiles file that contains multiple smiles.

	#set mountdir = `pwd`		#set mountdir = `pwd`

TBalius: /* new script in developmental version (DOCKBASE = ~tbalius/zzz.github/DOCK) */

2018-07-20T16:00:34Z

new script in developmental version (DOCKBASE = ~tbalius/zzz.github/DOCK)

← Older revision		Revision as of 16:00, 20 July 2018
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	$DOCKBASE/ligand/generate/build_ligand_tautprot_smiles_covalent.sh ${smi}.smi		$DOCKBASE/ligand/generate/build_ligand_tautprot_smiles_covalent.sh ${smi}.smi
	cd ../		cd ../
	~~endif~~		end


	== Do it by hand ==		== Do it by hand ==

TBalius at 15:50, 20 July 2018

2018-07-20T15:50:57Z

← Older revision		Revision as of 15:50, 20 July 2018
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	Sometimes you need to sample more ligand conformations when docking. If you have a saturated ring, you may want to explore alternative ring puckering. Here is how you can generate more ring conformations.		Sometimes you need to sample more ligand conformations when docking. If you have a saturated ring, you may want to explore alternative ring puckering. Here is how you can generate more ring conformations.

			== new script in developmental version (DOCKBASE = ~tbalius/zzz.github/DOCK) ==

			Here are two scripts that will perform additional ring puckering on a smiles file.

			This one is for standard docking (with spheres)
			$DOCKBASE/ligand/generate/build_ligand_tautprot_smiles.sh smi_file.smi

			This one is for covalent docking
			$DOCKBASE/ligand/generate/build_ligand_tautprot_smiles_covalent.sh smi_file.smi

			The smiles file contain one smiles. It should should be have all stereo chemistry defined and be in the right protonation and tautomerazation states.

			here is a wrapper script to run this on a smiles file that contains multiple smiles.

			#set mountdir = `pwd`
			#set
			source ~tbalius/.cshrc_main

			mkdir run_build_ligand_tautprot_smiles_covalent
			cd run_build_ligand_tautprot_smiles_covalent
			cp ../ligands.product.all.smi .

			split -l 1 ligands.product.all.smi ligands.product.

			ls ligands.product.??

			foreach smi (`ls ligands.product.??`)
			echo $smi
			mkdir ${smi}_dir
			cd ${smi}_dir
			cp ../${smi} ${smi}.smi
			$DOCKBASE/ligand/generate/build_ligand_tautprot_smiles_covalent.sh ${smi}.smi
			cd ../
			endif


			== Do it by hand ==

	1. Create a directory and cd into it.		1. Create a directory and cd into it.

TBalius at 17:57, 21 June 2018

2018-06-21T17:57:18Z

← Older revision		Revision as of 17:57, 21 June 2018
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			Sometimes you need to sample more ligand conformations when docking. If you have a saturated ring, you may want to explore alternative ring puckering. Here is how you can generate more ring conformations.


	1. Create a directory and cd into it.		1. Create a directory and cd into it.

TBalius at 17:48, 21 June 2018

2018-06-21T17:48:43Z

← Older revision		Revision as of 17:48, 21 June 2018
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	cd ZINC000001664886		cd ZINC000001664886

	(note that ~~ZINC000100008245~~ and ZINC000100008245 are the same molecule and both favor both substituents in axial~~, not equitorial~~).		(note that ZINC000001664886 and ZINC000100008245 are the same molecule and both favor both substituents in axial. ZINC000100004326 has one substituents in equatorial).

	2. Get the protonated smi from zinc:		2. Get the protonated smi from zinc:

TBalius at 17:45, 21 June 2018

2018-06-21T17:45:13Z

← Older revision		Revision as of 17:45, 21 June 2018
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	5. Split the whole mol2 file into individual conformers		5. Split the whole mol2 file into individual conformers

			sed -i 's/1 ZINC/ZINC/g' ZINC000001664886.mol2
			This command will remove the number 1 which appears before the ZINC name to make it compatible with the python scripted
			you can also manually edit the file to remove this number or even manually separate the files.
	python ~tbalius/zzz.scripts/separate_mol2_more10000_mod.py ZINC000001664886.mol2 test		python ~tbalius/zzz.scripts/separate_mol2_more10000_mod.py ZINC000001664886.mol2 test

TBalius at 17:19, 21 June 2018

2018-06-21T17:19:51Z

← Older revision		Revision as of 17:19, 21 June 2018
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	cd ZINC000001664886		cd ZINC000001664886

	(note that ZINC000100008245 and ZINC000100008245 are the same molecule and both favor both ~~substitution~~ in axial, not equitorial).		(note that ZINC000100008245 and ZINC000100008245 are the same molecule and both favor both substituents in axial, not equitorial).

	2. Get the protonated smi from zinc:		2. Get the protonated smi from zinc:

TBalius at 17:19, 21 June 2018

2018-06-21T17:19:04Z

← Older revision		Revision as of 17:19, 21 June 2018
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	1. Create a directory and cd into it		1. Create a directory and cd into it.
	mkdir ZINC000001664886		mkdir ZINC000001664886
	cd ZINC000001664886		cd ZINC000001664886

			(note that ZINC000100008245 and ZINC000100008245 are the same molecule and both favor both substitution in axial, not equitorial).

	2. Get the protonated smi from zinc:		2. Get the protonated smi from zinc:

Chasemwebb at 16:08, 21 June 2018

2018-06-21T16:08:15Z

← Older revision		Revision as of 16:08, 21 June 2018
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	3. For each isomer, give it a suffix, like _1, _2.		3. For each isomer, give it a suffix, like _1, _2.
	vim ZINC000001664886.smi		vim ZINC000001664886.smi
	4. run corina with enhanced sampling or ring puckers		4. run corina with enhanced sampling of ring puckers
	/nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=10,mc=10,wh ZINC000001664886.smi ZINC000001664886.mol2		/nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=10,mc=10,wh ZINC000001664886.smi ZINC000001664886.mol2