Minimize protein-ligand complex with AMBER - Revision history

TBalius: /* Step 4. Run minimization using the amber program PMEMD.cuda on a GPU machine */

2018-12-15T01:34:52Z

Step 4. Run minimization using the amber program PMEMD.cuda on a GPU machine

← Older revision		Revision as of 01:34, 15 December 2018
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	setenv AMBERHOME /nfs/soft/amber/amber14		setenv AMBERHOME /nfs/soft/amber/amber14
	setenv LD_LIBRARY_PATH ""		setenv LD_LIBRARY_PATH ""
	setenv LD_LIBRARY_PATH "/usr/local/cuda-6.0/lib64/:$LD_LIBRARY_PATH"		#setenv LD_LIBRARY_PATH "/usr/local/cuda-6.0/lib64/:$LD_LIBRARY_PATH"
			setenv LD_LIBRARY_PATH "/nfs/soft/cuda-6.5/lib64/:\$LD_LIBRARY_PATH"

	cat << EOF1 > ! 01mi.in		cat << EOF1 > ! 01mi.in
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	setenv AMBERHOME /nfs/soft/amber/amber14		setenv AMBERHOME /nfs/soft/amber/amber14
	setenv LD_LIBRARY_PATH ""		setenv LD_LIBRARY_PATH ""
	setenv LD_LIBRARY_PATH "/usr/local/cuda-6.0/lib64/:$LD_LIBRARY_PATH"		#setenv LD_LIBRARY_PATH "/usr/local/cuda-6.0/lib64/:$LD_LIBRARY_PATH"
			setenv LD_LIBRARY_PATH "/nfs/soft/cuda-6.5/lib64/:\$LD_LIBRARY_PATH"

	cat << EOF1 > ! 01mi.lig.in		cat << EOF1 > ! 01mi.lig.in

TBalius: /* Step 2. Prepare ligand charges and force field. */

2018-04-16T20:54:34Z

Step 2. Prepare ligand charges and force field.

← Older revision		Revision as of 20:54, 16 April 2018
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	==Step 2. Prepare ligand charges and force field. ==		==Step 2. Prepare ligand charges and force field. ==

	Here is a script that calls antechamber to prepare ligand charges and force field.		Here is a script that calls antechamber to prepare ligand charges and force field. Here are three things to be mindful of:
	The flag "-nc" specifies the net charge of the small molecule be sure to replace this with the correct value.		* The flag "-nc" specifies the net charge of the small molecule be sure to replace this with the correct value.
	The ligand must have hydrogen's added.		* The ligand must have hydrogen's added.
	Also, the atom typing is dependent on the 3D coordinates.		* Also, the atom typing is dependent on the 3D coordinates.

	You can call openbabel to calculate charges, for example:		You can call openbabel to calculate charges, for example:

TBalius: /* Step 2. Prepare ligand charges and force field. */

2018-04-06T20:16:03Z

Step 2. Prepare ligand charges and force field.

← Older revision		Revision as of 20:16, 6 April 2018
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	# add GASTEIGER charges		# add GASTEIGER charges
	obabel -ipdb lig.pdb -omol2 -O lig.gast.mol2 -charge		obabel -ipdb lig.pdb -omol2 -O lig.gast.mol2 -charge
	cat lig.gast.mol2 \| awk 'BEGIN{sum=0};{if(NF==9){print $9;sum=sum+$9}};END{printf"\nsum=%6.2f\n\n",sum}'		cat lig.gast.mol2 \| awk 'BEGIN{sum=0};{if(NF==9){print $9;sum=sum+$9}};END{printf"\nsum=%.0f\n\n",sum}'
	set chrg = `cat lig.gast.mol2 \| awk 'BEGIN{sum=0};{if(NF==9){sum=sum+$9}};END{printf"%6.2f\n",sum}'`		set chrg = `cat lig.gast.mol2 \| awk 'BEGIN{sum=0};{if(NF==9){sum=sum+$9}};END{printf"%.0f\n",sum}'`

TBalius: /* Step 2. Prepare ligand charges and force field. */

2018-04-06T20:09:14Z

Step 2. Prepare ligand charges and force field.

← Older revision		Revision as of 20:09, 6 April 2018
Line 48:		Line 48:
	==Step 2. Prepare ligand charges and force field. ==		==Step 2. Prepare ligand charges and force field. ==

	Here is a script that calls antechamber.		Here is a script that calls antechamber to prepare ligand charges and force field.
	The flag "-nc" specifies the net charge of the small molecule be sure to replace this with the correct value.		The flag "-nc" specifies the net charge of the small molecule be sure to replace this with the correct value.
	Also the atom typing is dependent on the 3D coordinates.		The ligand must have hydrogen's added.
			Also, the atom typing is dependent on the 3D coordinates.

			You can call openbabel to calculate charges, for example:
			# add GASTEIGER charges
			obabel -ipdb lig.pdb -omol2 -O lig.gast.mol2 -charge
			cat lig.gast.mol2 \| awk 'BEGIN{sum=0};{if(NF==9){print $9;sum=sum+$9}};END{printf"\nsum=%6.2f\n\n",sum}'
			set chrg = `cat lig.gast.mol2 \| awk 'BEGIN{sum=0};{if(NF==9){sum=sum+$9}};END{printf"%6.2f\n",sum}'`


	Create a script called "run.002.ligprep.antechamber.csh".		Create a script called "run.002.ligprep.antechamber.csh".
	#! /bin/tcsh		#! /bin/tcsh
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	$AMBERHOME/bin/antechamber -i lig.ante.charge.mol2 -fi mol2 -o lig.ante.charge.prep -fo prepi		$AMBERHOME/bin/antechamber -i lig.ante.charge.mol2 -fi mol2 -o lig.ante.charge.prep -fo prepi
	$AMBERHOME/bin/parmchk -i lig.ante.charge.prep -f prepi -o lig.ante.charge.frcmod		$AMBERHOME/bin/parmchk -i lig.ante.charge.prep -f prepi -o lig.ante.charge.frcmod


	==Step 3. Prepare the coordinate file and topology-and-parameter files for amber. ==		==Step 3. Prepare the coordinate file and topology-and-parameter files for amber. ==

TBalius: /* Step 4. Run minimization using the amber program PMEMD.cuda on a GPU machine */

2018-04-06T00:47:57Z

Step 4. Run minimization using the amber program PMEMD.cuda on a GPU machine

← Older revision		Revision as of 00:47, 6 April 2018
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	#\$ -o stdout		#\$ -o stdout
	#\$ -e stderr		#\$ -e stderr

	cd $pwd		cd $pwd

TBalius: /* Step 4. Run minimization using the amber program PMEMD.cuda on a GPU machine */

2018-04-06T00:47:32Z

Step 4. Run minimization using the amber program PMEMD.cuda on a GPU machine

← Older revision		Revision as of 00:47, 6 April 2018
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	set pwd = `pwd`		set pwd = `pwd`
	#cd $pwd		#cd $pwd

	cat << EOF > ! qsub.sander.csh		cat << EOF > ! qsub.sander.csh
	#\$ -S /bin/csh		#\$ -S /bin/csh

TBalius: /* Step 4. Run minimization using the amber program PMEMD.cuda on a GPU machine */

2018-04-06T00:47:08Z

Step 4. Run minimization using the amber program PMEMD.cuda on a GPU machine

← Older revision		Revision as of 00:47, 6 April 2018
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	#\$ -S /bin/csh		#\$ -S /bin/csh
	#\$ -cwd		#\$ -cwd
			#\$ -q gpu.q
	#\$ -o stdout		#\$ -o stdout
	#\$ -e stderr		#\$ -e stderr

	cd $pwd		cd $pwd

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	#\$ -S /bin/csh		#\$ -S /bin/csh
	#\$ -cwd		#\$ -cwd
			#\$ -q gpu.q
	#\$ -o stdout		#\$ -o stdout
	#\$ -e stderr		#\$ -e stderr

TBalius: /* Step 4. Run minimization using the amber program PMEMD.cuda on a GPU machine */

2018-04-06T00:40:27Z

Step 4. Run minimization using the amber program PMEMD.cuda on a GPU machine

← Older revision		Revision as of 00:40, 6 April 2018
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	#$AMBERHOME/bin/pmemd.cuda -O -i 01mi.in -o 01mi.out -p com.leap.prm7 -c com.leap.rst7 -ref com.leap.rst7 -x 01mi.mdcrd -inf 01mi.info -r 01mi.rst7		#$AMBERHOME/bin/pmemd.cuda -O -i 01mi.in -o 01mi.out -p com.leap.prm7 -c com.leap.rst7 -ref com.leap.rst7 -x 01mi.mdcrd -inf 01mi.info -r 01mi.rst7
			#$AMBERHOME/bin/sander -O -i 01mi.in -o 01mi.out -p com.leap.prm7 -c com.leap.rst7 -ref com.leap.rst7 -x 01mi.mdcrd -inf 01mi.info -r 01mi.rst7

	set pwd = `pwd`		set pwd = `pwd`
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	cd $pwd		cd $pwd
	$AMBERHOME/bin/~~sander~~ -O -i 01mi.in -o 01mi.out -p com.leap.prm7 -c com.leap.rst7 -ref com.leap.rst7 -x 01mi.mdcrd -inf 01mi.info -r 01mi.rst7
			$AMBERHOME/bin/pmemd.cuda -O -i 01mi.in -o 01mi.out -p com.leap.prm7 -c com.leap.rst7 -ref com.leap.rst7 -x 01mi.mdcrd -inf 01mi.info -r 01mi.rst7

	EOF		EOF
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	#$AMBERHOME/bin/pmemd.cuda -O -i 01mi.in -o 01mi.out -p com.leap.prm7 -c com.leap.rst7 -ref com.leap.rst7 -x 01mi.mdcrd -inf 01mi.info -r 01mi.rst7		#$AMBERHOME/bin/pmemd.cuda -O -i 01mi.in -o 01mi.out -p com.leap.prm7 -c com.leap.rst7 -ref com.leap.rst7 -x 01mi.mdcrd -inf 01mi.info -r 01mi.rst7
			#$AMBERHOME/bin/sander -O -i 01mi.lig.in -o 01mi.lig.out -p lig.leap.prm7 -c lig.leap.rst7 -ref lig.leap.rst7 -x 01mi.lig.mdcrd -inf 01mi.lig.info -r 01mi.lig.rst7

	set pwd = `pwd`		set pwd = `pwd`
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	cd $pwd		cd $pwd
	$AMBERHOME/bin/~~sander~~ -O -i 01mi.lig.in -o 01mi.lig.out -p lig.leap.prm7 -c lig.leap.rst7 -ref lig.leap.rst7 -x 01mi.lig.mdcrd -inf 01mi.lig.info -r 01mi.lig.rst7		$AMBERHOME/bin/pmemd.cuda -O -i 01mi.lig.in -o 01mi.lig.out -p lig.leap.prm7 -c lig.leap.rst7 -ref lig.leap.rst7 -x 01mi.lig.mdcrd -inf 01mi.lig.info -r 01mi.lig.rst7

	EOF		EOF

	qsub qsub.sander.lig.csh		qsub qsub.sander.lig.csh

	== Step 5. Convert to pdb for easy visualization. ==		== Step 5. Convert to pdb for easy visualization. ==

TBalius at 17:19, 2 April 2018

2018-04-02T17:19:44Z

← Older revision		Revision as of 17:19, 2 April 2018
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	echo "Warning: No ligand or peptid."		echo "Warning: No ligand or peptid."
	endif		endif

			run the script as follows:

			csh run.001.be_balsti_reduce.csh

	==Step 2. Prepare ligand charges and force field. ==		==Step 2. Prepare ligand charges and force field. ==

TBalius at 17:18, 2 April 2018

2018-04-02T17:18:51Z

← Older revision		Revision as of 17:18, 2 April 2018
Line 48:		Line 48:
	Also the atom typing is dependent on the 3D coordinates.		Also the atom typing is dependent on the 3D coordinates.

	~~cat~~ run.002.ligprep.antechamber.csh ~~\| awk '{print~~ " ~~" $0}'~~		Create a script called "run.002.ligprep.antechamber.csh".
	#! /bin/tcsh		#! /bin/tcsh

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	==Step 3. Prepare the coordinate file and topology-and-parameter files for amber. ==		==Step 3. Prepare the coordinate file and topology-and-parameter files for amber. ==

	~~cat~~ run.003.tleap.csh ~~\| awk '{print~~ " ~~" $0}'~~		Create a script called "run.003.tleap.csh".

	setenv AMBERHOME /nfs/soft/amber/amber14		setenv AMBERHOME /nfs/soft/amber/amber14
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	==Step 4. Run minimization using the amber program PMEMD.cuda on a GPU machine ==		==Step 4. Run minimization using the amber program PMEMD.cuda on a GPU machine ==

	~~cat~~ run.004.pmemd_cuda_min.csh ~~\| awk '{print "~~ " ~~$0}'~~		Create a script called "run.004.pmemd_cuda_min.csh"

	#setenv AMBERHOME /nfs/soft/amber/amber14		#setenv AMBERHOME /nfs/soft/amber/amber14
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	You might want to also minimize the ligand on its own:		You might want to also minimize the ligand on its own:

	~~cat~~ run.004.pmemd_cuda_min.lig.csh ~~\| awk '{print~~ " ~~" $0}'~~		Create a script called "run.004.pmemd_cuda_min.lig.csh".

	#setenv AMBERHOME /nfs/soft/amber/amber14		#setenv AMBERHOME /nfs/soft/amber/amber14