On 1/30/14, 11:12 AM, bipin singh wrote:
The protonated and deprotonated states will differ only in terms of
presence or absence of hydrogens, thus in B state only that hydrogen atom
which is intended to be transformed from protonated to deprotonated state
will be altered in the terms of electrostatic and vdw parameters.
Incorrect. The atom types and charges for the whole carboxylate moiety are
affected by the removal of the proton. Only H becomes a dummy atom, but the C
and both O atoms of the resulting COO- group will be different depending on
protonation state. See GLU/GLUH in aminoacids.rtp.
-Justin
On Thu, Jan 30, 2014 at 8:55 PM, Ozbil, Mehmet <m.oz...@umiami.edu> wrote:
I see Bipin,
Thanks. One quick question though, am I going to change the charges to
zero or all atoms to DUM atoms for all the atoms in B state or just for the
hydrogen that will be transferred between the states (the atom where the B
state was missing before):
16 opls_270 77 GLU HE2 5 0.45 1.008
Thanks again.
Mehmet
________________________________________
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of bipin
singh <bipinel...@gmail.com>
Sent: Wednesday, January 29, 2014 10:46 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] free energy calculations for reference state for
constant pH MD simulations...
You have to define the B state parameters for your deprotonated state
explicitly.
The following line in your topology does not have the parameters for the B
state.
16 opls_270 77 GLU HE2 5 0.45 1.008
You have to set the charges zero in the B state (if you want to consider
the change in electrostatic term only during deprotonation) or else change
it to DUM atom (if you want to change both the vdw and electrostatics terms
during deprotonation).
On Wed, Jan 29, 2014 at 8:15 PM, Ozbil, Mehmet <m.oz...@umiami.edu> wrote:
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-boun...@maillist.sys.kth.se <
gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of bipin
singh <bipinel...@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.oz...@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
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==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
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University of Maryland, Baltimore
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