Minimize protein-covalent ligand complex with AMBER - Revision history

TBalius at 13:29, 26 August 2019

2019-08-26T13:29:48Z

← Older revision		Revision as of 13:29, 26 August 2019
Line 15:		Line 15:
	(3.1) for the receptor, rec.pdb:		(3.1) for the receptor, rec.pdb:

	Change the covalent cysteine to reduce name ~~CYM~~.		Change the covalent cysteine to reduce name CYB.

	Here is a modified cystiene residue (this is without a charge and without a hydrogen):		Here is a modified cystiene residue (this is without a charge and without a hydrogen):

	cat ~~CYM~~.prep		cat CYB.prep

	0 0 2		0 0 2
Line 25:		Line 25:
	CYSTEINE without h and without charge for covalent		CYSTEINE without h and without charge for covalent

	~~CYM~~ INT 0		CYB INT 0
	CORR OMIT DU BEG		CORR OMIT DU BEG
	0.00000		0.00000
Line 310:		Line 310:


	Modify the prep file to remove the cysteine side chain. Also add partial charge to covalent carbon to make the Cysteine (~~CYM~~) + covalent ligand an integer.		Modify the prep file to remove the cysteine side chain. Also add partial charge to covalent carbon to make the Cysteine (CYB) + covalent ligand an integer.

	diff lig/lig.ante.charge.prep lig/lig.ante.charge.mod.prep		diff lig/lig.ante.charge.prep lig/lig.ante.charge.mod.prep
Line 385:		Line 385:
	loadamberprep lig2/lig.ante.charge.prep		loadamberprep lig2/lig.ante.charge.prep

	loadamberprep ~~CYM~~.prep		loadamberprep CYB.prep

	# load pdb file		# load pdb file

TBalius at 19:55, 3 January 2019

2019-01-03T19:55:09Z

← Older revision		Revision as of 19:55, 3 January 2019
Line 77:		Line 77:
	(3.2) for a covalent ligand, lig.pdb:		(3.2) for a covalent ligand, lig.pdb:

	~~keep~~ the ~~sidechain~~ of the ~~mofifed cystien~~:		Keep the side chain of the modified cysteine:

	cat 94F_bkup.pdb		cat 94F_bkup.pdb
Line 117:		Line 117:
	ATOM 1416 CL 94F A 203 19.224 -0.960 23.165 1.00 29.22 CL		ATOM 1416 CL 94F A 203 19.224 -0.960 23.165 1.00 29.22 CL

	~~change~~ and make the numbering and naming consistent:		Change and make the numbering and naming consistent:

	cat 94F.pdb		cat 94F.pdb
Line 284:		Line 284:
	END		END

	~~run~~ the following script:		Run the following script:

	cat run.002.ligprep.antechamber.csh		cat run.002.ligprep.antechamber.csh
Line 310:		Line 310:


	~~modify~~ the prep file to remove the cysteine side chain. Also add partial charge to covalent carbon to make the Cysteine (CYM) + covalent ligand an integer.		Modify the prep file to remove the cysteine side chain. Also add partial charge to covalent carbon to make the Cysteine (CYM) + covalent ligand an integer.

	diff lig/lig.ante.charge.prep lig/lig.ante.charge.mod.prep		diff lig/lig.ante.charge.prep lig/lig.ante.charge.mod.prep
Line 331:		Line 331:
	Add hydrogens to gdp is chimera.		Add hydrogens to gdp is chimera.

	~~build~~ the prep and frcmod files with antechamber:		Build the prep and frcmod files with antechamber:

	cat run.002.ligprep.antechamber_gdp.csh		cat run.002.ligprep.antechamber_gdp.csh

TBalius at 19:47, 3 January 2019

2019-01-03T19:47:08Z

← Older revision		Revision as of 19:47, 3 January 2019
Line 162:		Line 162:


	Save the ~~protinated~~ molecule in pdb format and rename the atoms:		Save the protonated molecule in pdb format and rename the atoms:

	cat 94F.full_mod_num.pdb		cat 94F.full_mod_num.pdb

TBalius at 19:23, 17 December 2018

2018-12-17T19:23:20Z

← Older revision		Revision as of 19:23, 17 December 2018
Line 462:		Line 462:

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

			Visualize the minimized coordinates with Chimera or VMD, you can first convert the files to pdb format with the following commands:

			$AMBERHOME/bin/ambpdb -p com.leap.prm7 < 01mi.rst7 > 01mi.pdb

			$AMBERHOME/bin/ambpdb -p com.leap.prm7 < com.leap.rst7 > com.leap.pdb

TBalius at 19:14, 17 December 2018

2018-12-17T19:14:44Z

Show changes

TBalius at 19:10, 17 December 2018

2018-12-17T19:10:38Z

@@ Line 298: / Line 298: @@
-(3.3) and a receptor, rec.pdb:
+(3.3) and for the receptor, rec.pdb:
 Here is a modified cystiene residue (this is without a charge and without a hydrogen):
@@ Line 357: / Line 359: @@
 These parameter values were taken from the gaff force field (/nfs/soft/amber/amber14/dat/leap/parm/gaff.dat).

TBalius at 19:07, 17 December 2018

2018-12-17T19:07:06Z

← Older revision		Revision as of 19:07, 17 December 2018
Line 11:		Line 11:


	(3) Manually create 3 files using your favorate text editor:		(3) Manually create 3 files using your favorate text editor: a covalent ligand, a co-facotor and a receptor file.

	a covalent ligand, lig.pdb:		(3.1) for a covalent ligand, lig.pdb:

	keep the sidechain of the mofifed cystien:		keep the sidechain of the mofifed cystien:
Line 233:		Line 233:


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

	rm lig; mkdir lig; cd lig		rm lig; mkdir lig; cd lig
Line 265:		Line 265:
	> 12 C18 c3 M 3 2 1 1.617 102.332 -80.293 -0.037200		> 12 C18 c3 M 3 2 1 1.617 102.332 -80.293 -0.037200

	a co-factory (gdp), gdp.pdb:		(3.2) for a co-factory (gdp), gdp.pdb:

			Add hydrogens to gdp is chimera.

			build the prep and frcmod files with antechamber:

			cat run.002.ligprep.antechamber_gdp.csh

			#! /bin/tcsh


			set workdir = `pwd`
			cd $workdir


			setenv AMBERHOME /nfs/soft/amber/amber14

			rm lig2; mkdir lig2; cd lig2

			#cp $workdir/xtal-lig.pdb lig.pdb
			#cp $workdir/33443.pdb lig.pdb
			cp $workdir/gdp_h.pdb lig.pdb
			#sed -i 's/<0> /LIG/g' lig1.mol2

			$AMBERHOME/bin/antechamber -i lig.pdb -fi pdb -o lig.ante.mol2 -fo mol2

			$AMBERHOME/bin/antechamber -i lig.ante.mol2 -fi mol2 -o lig.ante.charge.mol2 -fo mol2 -c bcc -at sybyl -nc -3
			$AMBERHOME/bin/antechamber -i lig.ante.mol2 -fi mol2 -o lig.ante.pdb -fo pdb
			$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



	and a receptor, rec.pdb:		(3.3) and a receptor, rec.pdb:

	Here is a modified cystiene residue (this is without a charge and without a hydrogen):		Here is a modified cystiene residue (this is without a charge and without a hydrogen):

TBalius at 19:01, 17 December 2018

2018-12-17T19:01:02Z

Show changes

TBalius at 17:58, 17 December 2018

2018-12-17T17:58:47Z

← Older revision		Revision as of 17:58, 17 December 2018
Line 97:		Line 97:
	Uses chimera to add hydrogens:		Uses chimera to add hydrogens:

			[[File:2018_12_coval1.png\|thumb\|center\|500px\|Use chimera to add hydrogens]]

TBalius: Created page with " This is for ligands that modify a specific residue. (1) Make a directory: mkdir coval_min cd coval_min/ (2) Download pdb file from the web: wget https://files.rcsb...."

2018-12-17T17:55:14Z

Created page with " This is for ligands that modify a specific residue. (1) Make a directory: mkdir coval_min cd coval_min/ (2) Download pdb file from the web: wget https://files.rcsb...."

New page

This is for ligands that modify a specific residue.

(1) Make a directory:
mkdir coval_min
cd coval_min/

(2) Download pdb file from the web:
wget https://files.rcsb.org/view/5YY1.pdb

(3) Manually create 3 files using your favorate text editor:

a covalent ligand, lig.pdb:

keep the sidechain of the mofifed cystien:

cat 94F_bkup.pdb

ATOM 89 CA CYS A 12 29.215 -1.013 17.747 1.00 23.10 C
ATOM 92 CB CYS A 12 30.264 -1.172 18.849 1.00 23.68 C
ATOM 93 SG CYS A 12 29.632 -1.020 20.503 1.00 25.01 S
ATOM 1385 C31 94F A 203 16.511 -4.125 24.817 1.00 32.17 C
ATOM 1386 C30 94F A 203 15.606 -4.260 23.787 1.00 32.36 C
ATOM 1387 C32 94F A 203 17.840 -3.910 24.531 1.00 31.54 C
ATOM 1388 C29 94F A 203 16.037 -4.183 22.484 1.00 32.47 C
ATOM 1389 C19 94F A 203 21.614 -2.199 22.881 1.00 29.12 C
ATOM 1390 C5 94F A 203 23.964 -5.464 22.540 1.00 29.57 C
ATOM 1391 C18 94F A 203 22.453 -3.293 22.771 1.00 29.13 C
ATOM 1392 C23 94F A 203 18.284 -3.829 23.223 1.00 31.43 C
ATOM 1393 C22 94F A 203 19.692 -3.612 23.019 1.00 29.79 C
ATOM 1394 C24 94F A 203 17.372 -3.972 22.203 1.00 32.05 C
ATOM 1395 C3 94F A 203 21.900 -4.565 22.770 1.00 29.39 C
ATOM 1396 C2 94F A 203 20.533 -4.693 22.895 1.00 29.45 C
ATOM 1397 C20 94F A 203 20.247 -2.347 23.012 1.00 29.51 C
ATOM 1398 C7 94F A 203 23.836 -3.189 22.644 1.00 28.94 C
ATOM 1399 C14 94F A 203 29.536 0.583 20.690 1.00 25.47 C
ATOM 1400 C13 94F A 203 28.376 1.143 21.474 1.00 26.40 C
ATOM 1401 C12 94F A 203 27.093 0.850 20.795 1.00 26.10 C
ATOM 1402 C9 94F A 203 23.979 -0.953 21.731 1.00 28.62 C
ATOM 1403 C17 94F A 203 25.969 -2.149 22.595 1.00 29.17 C
ATOM 1404 C10 94F A 203 25.024 -0.390 20.794 1.00 28.12 C
ATOM 1405 C16 94F A 203 26.678 -0.809 22.586 1.00 28.22 C
ATOM 1406 C25 94F A 203 17.826 -3.897 20.794 1.00 32.91 C
ATOM 1407 N4 94F A 203 22.652 -5.665 22.653 1.00 29.29 N
ATOM 1408 N6 94F A 203 24.595 -4.289 22.534 1.00 29.70 N
ATOM 1409 N8 94F A 203 24.523 -1.948 22.642 1.00 29.33 N
ATOM 1410 N11 94F A 203 26.238 0.005 21.476 1.00 27.18 N
ATOM 1411 O15 94F A 203 26.847 1.362 19.713 1.00 25.34 O
ATOM 1412 F1 94F A 203 19.995 -5.935 22.878 1.00 29.69 F
ATOM 1413 F26 94F A 203 16.791 -3.770 19.931 1.00 34.77 F
ATOM 1414 F27 94F A 203 18.674 -2.862 20.538 1.00 31.92 F
ATOM 1415 F28 94F A 203 18.495 -5.026 20.445 1.00 33.49 F
ATOM 1416 CL 94F A 203 19.224 -0.960 23.165 1.00 29.22 CL

change and make the numbering and naming consistent:

cat 94F.pdb

ATOM 1382 CA LIG A 203 29.215 -1.013 17.747 1.00 23.10 C
ATOM 1383 CB LIG A 203 30.264 -1.172 18.849 1.00 23.68 C
ATOM 1384 SG LIG A 203 29.632 -1.020 20.503 1.00 25.01 S
ATOM 1385 C31 LIG A 203 16.511 -4.125 24.817 1.00 32.17 C
ATOM 1386 C30 LIG A 203 15.606 -4.260 23.787 1.00 32.36 C
ATOM 1387 C32 LIG A 203 17.840 -3.910 24.531 1.00 31.54 C
ATOM 1388 C29 LIG A 203 16.037 -4.183 22.484 1.00 32.47 C
ATOM 1389 C19 LIG A 203 21.614 -2.199 22.881 1.00 29.12 C
ATOM 1390 C5 LIG A 203 23.964 -5.464 22.540 1.00 29.57 C
ATOM 1391 C18 LIG A 203 22.453 -3.293 22.771 1.00 29.13 C
ATOM 1392 C23 LIG A 203 18.284 -3.829 23.223 1.00 31.43 C
ATOM 1393 C22 LIG A 203 19.692 -3.612 23.019 1.00 29.79 C
ATOM 1394 C24 LIG A 203 17.372 -3.972 22.203 1.00 32.05 C
ATOM 1395 C3 LIG A 203 21.900 -4.565 22.770 1.00 29.39 C
ATOM 1396 C2 LIG A 203 20.533 -4.693 22.895 1.00 29.45 C
ATOM 1397 C20 LIG A 203 20.247 -2.347 23.012 1.00 29.51 C
ATOM 1398 C7 LIG A 203 23.836 -3.189 22.644 1.00 28.94 C
ATOM 1399 C14 LIG A 203 29.536 0.583 20.690 1.00 25.47 C
ATOM 1400 C13 LIG A 203 28.376 1.143 21.474 1.00 26.40 C
ATOM 1401 C12 LIG A 203 27.093 0.850 20.795 1.00 26.10 C
ATOM 1402 C9 LIG A 203 23.979 -0.953 21.731 1.00 28.62 C
ATOM 1403 C17 LIG A 203 25.969 -2.149 22.595 1.00 29.17 C
ATOM 1404 C10 LIG A 203 25.024 -0.390 20.794 1.00 28.12 C
ATOM 1405 C16 LIG A 203 26.678 -0.809 22.586 1.00 28.22 C
ATOM 1406 C25 LIG A 203 17.826 -3.897 20.794 1.00 32.91 C
ATOM 1407 N4 LIG A 203 22.652 -5.665 22.653 1.00 29.29 N
ATOM 1408 N6 LIG A 203 24.595 -4.289 22.534 1.00 29.70 N
ATOM 1409 N8 LIG A 203 24.523 -1.948 22.642 1.00 29.33 N
ATOM 1410 N11 LIG A 203 26.238 0.005 21.476 1.00 27.18 N
ATOM 1411 O15 LIG A 203 26.847 1.362 19.713 1.00 25.34 O
ATOM 1412 F1 LIG A 203 19.995 -5.935 22.878 1.00 29.69 F
ATOM 1413 F26 LIG A 203 16.791 -3.770 19.931 1.00 34.77 F
ATOM 1414 F27 LIG A 203 18.674 -2.862 20.538 1.00 31.92 F
ATOM 1415 F28 LIG A 203 18.495 -5.026 20.445 1.00 33.49 F
ATOM 1416 CL LIG A 203 19.224 -0.960 23.165 1.00 29.22 CL

Uses chimera to add hydrogens:

a co-factory (gdp), gdp.pdb:

and a receptor, rec.pdb:

Here is a modified cystiene residue (this is without a charge and without a hydrogen):

cat CYM.prep

0 0 2

CYSTEINE without h and without charge for covalent

CYM INT 0
CORR OMIT DU BEG
0.00000
1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000
2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000
3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000
4 N N M 3 2 1 1.335 116.600 180.000 -0.41570
5 H H E 4 3 2 1.010 119.800 0.000 0.27190
6 CA CX M 4 3 2 1.449 121.900 180.000 0.02130
7 HA H1 E 6 4 3 1.090 109.500 300.000 0.11240
8 CB 2C 3 6 4 3 1.525 111.100 60.000 -0.12310
9 HB2 H1 E 8 6 4 1.090 109.500 300.000 0.11120
10 HB3 H1 E 8 6 4 1.090 109.500 60.000 0.11120
11 SG SH E 8 6 4 1.810 116.000 180.000 -0.23580
12 C C M 6 4 3 1.522 111.100 180.000 0.59730
13 O O E 12 6 4 1.229 120.500 0.000 -0.56790

IMPROPER
-M CA N H
CA +M C O

DONE
STOP