[gmx-users] free energy calculations for reference state for constant pH MD simulations...
Ozbil, Mehmet
m.ozbil at umiami.edu
Wed Jan 29 17:17:54 CET 2014
Thanks Bipin for the reply.
I went through the Gromacs manual, and thought that I managed to incorporate two states (protonated and deprotonated) in my topology file. Can anyone who has done it before tell me if I defined both A and B states correctly in my .top file.
;
; File 'GLUA_prot_OPLS_p.top' was generated
; By user: onbekend (0)
; On host: onbekend
; At date: Tue Jan 28 13:49:17 2014
;
; This is a standalone topology file
;
; It was generated using program:
; pdb2gmx - VERSION 4.5.4
;
; Command line was:
; /home/apps/fas/Apps/Gromacs/gromacs-4.5.4-intel/bin//pdb2gmx -f GLUA_prot_OPLS.pdb -p GLUA_prot_OPLS_p.top -o GLUA_prot_OPLS_p.gro -inter
;
; Force field was read from the standard Gromacs share directory.
;
; Include forcefield parameters
#include "oplsaa.ff/forcefield.itp"
[ moleculetype ]
; Name nrexcl
Protein_chain_A 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 77 GLU rtp GLUH q 0.0
1 opls_287 77 GLU N 1 -0.3 14.0067 opls_287 -0.3 14.0067
2 opls_290 77 GLU H1 1 0.33 1.008 opls_290 0.33 1.008
3 opls_290 77 GLU H2 1 0.33 1.008 opls_290 0.33 1.008
4 opls_290 77 GLU H3 1 0.33 1.008 opls_290 0.33 1.008
5 opls_299 77 GLU CA 1 0.15 12.011 opls_299 0.15 12.011
6 opls_140 77 GLU HA 1 0.06 1.008 opls_140 0.06 1.008
7 opls_136 77 GLU CB 2 -0.12 12.011 opls_136 -0.12 12.011
8 opls_140 77 GLU HB1 2 0.06 1.008 opls_140 0.06 1.008
9 opls_140 77 GLU HB2 2 0.06 1.008 opls_140 0.06 1.008
10 opls_136 77 GLU CG 3 -0.12 12.011 opls_136 -0.12 12.011
11 opls_140 77 GLU HG1 3 0.06 1.008 opls_140 0.06 1.008
12 opls_140 77 GLU HG2 3 0.06 1.008 opls_140 0.06 1.008
13 opls_267 77 GLU CD 4 0.52 12.011 opls_267 0.52 12.011
14 opls_269 77 GLU OE1 4 -0.44 15.9994 opls_269 -0.44 15.9994
15 opls_268 77 GLU OE2 5 -0.53 15.9994 opls_268 -0.53 15.9994
16 opls_270 77 GLU HE2 5 0.45 1.008
17 opls_271 77 GLU C 6 0.7 12.011 opls_271 0.7 12.011
18 opls_272 77 GLU O1 6 -0.8 15.9994 opls_272 -0.8 15.9994
19 opls_272 77 GLU O2 6 -0.8 15.9994 opls_272 -0.8 15.9994
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1
1 3 1
1 4 1
1 5 1
5 6 1
5 7 1
5 17 1
7 8 1
7 9 1
7 10 1
10 11 1
10 12 1
10 13 1
13 14 1
13 15 1
15 16 1
17 18 1
17 19 1
[ pairs ]
; ai aj funct c0 c1 c2 c3
1 8 1
1 9 1
1 10 1
1 18 1
1 19 1
2 6 1
2 7 1
2 17 1
3 6 1
3 7 1
3 17 1
4 6 1
4 7 1
4 17 1
5 11 1
5 12 1
5 13 1
6 8 1
6 9 1
6 10 1
6 18 1
6 19 1
7 14 1
7 15 1
7 18 1
7 19 1
8 11 1
8 12 1
8 13 1
8 17 1
9 11 1
9 12 1
9 13 1
9 17 1
10 16 1
10 17 1
11 14 1
11 15 1
12 14 1
12 15 1
14 16 1
[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 3 1
2 1 4 1
2 1 5 1
3 1 4 1
3 1 5 1
4 1 5 1
1 5 6 1
1 5 7 1
1 5 17 1
6 5 7 1
6 5 17 1
7 5 17 1
5 7 8 1
5 7 9 1
5 7 10 1
8 7 9 1
8 7 10 1
9 7 10 1
7 10 11 1
7 10 12 1
7 10 13 1
11 10 12 1
11 10 13 1
12 10 13 1
10 13 14 1
10 13 15 1
14 13 15 1
13 15 16 1
5 17 18 1
5 17 19 1
18 17 19 1
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
2 1 5 6 3
2 1 5 7 3
2 1 5 17 3
3 1 5 6 3
3 1 5 7 3
3 1 5 17 3
4 1 5 6 3
4 1 5 7 3
4 1 5 17 3
1 5 7 10 3 dih_GLU_chi1_N_C_C_C
17 5 7 10 3 dih_GLU_chi1_C_C_C_CO
1 5 7 8 3
1 5 7 9 3
6 5 7 8 3
6 5 7 9 3
6 5 7 10 3
17 5 7 8 3
17 5 7 9 3
1 5 17 18 3
1 5 17 19 3
6 5 17 18 3
6 5 17 19 3
7 5 17 18 3
7 5 17 19 3
5 7 10 11 3
5 7 10 12 3
5 7 10 13 3
8 7 10 11 3
8 7 10 12 3
8 7 10 13 3
9 7 10 11 3
9 7 10 12 3
9 7 10 13 3
7 10 13 14 3
7 10 13 15 3
11 10 13 14 3
11 10 13 15 3
12 10 13 14 3
12 10 13 15 3
10 13 15 16 3 dih_sidechain_COOH_C_C_O_H
14 13 15 16 3 dih_sidechain_COOH_O_C_O_H
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3
5 18 17 19 1 improper_O_C_X_Y
10 14 13 15 1 improper_O_C_X_Y
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include water topology
#include "oplsaa.ff/tip3p.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include topology for ions
#include "oplsaa.ff/ions.itp"
[ system ]
; Name
Protein in water
[ molecules ]
; Compound #mols
Protein_chain_A 1
SOL 4135
Thanks,
Mehmet
________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of bipin singh <bipinelmat at gmail.com>
Sent: Tuesday, January 28, 2014 2:46 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] free energy calculations for reference state for constant pH MD simulations...
See the section "5.7.4 Topologies for free energy calculations" in Gromacs
4.6.5 manual.
On Tue, Jan 28, 2014 at 3:09 AM, Ozbil, Mehmet <m.ozbil at umiami.edu> wrote:
> Hello,
>
> I am trying to run constant pH MD with GROMACS, and started with the TI
> free energy calculations. I am following Justin Lemkul`s free energy
> calculation tutorial, and assuming that the free energy calculations will
> be similar to calculate the protonation energy of titratable amino acids
> such as GLU or HIS.
>
> My question is that, while scanning the lambda values for the free energy
> calculations do I need to define both protonated and deprotonated states of
> GLU in the same .top and .pdb file, or I just use one .top and one .pdb
> file and by changing the lambda values from 0.0 to 1.0 it does the
> deprotonation itself. If I need to incorporate the two states in one .top
> and .pdb file can anyone help with how to do that?
>
> Thanks,
> Mehmet Ozbil
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
--
*--------------------Thanks and Regards,Bipin Singh*
--
Gromacs Users mailing list
* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users
mailing list