[gmx-users] free energy calculations for reference state for constant pH MD simulations...
Ozbil, Mehmet
m.ozbil at umiami.edu
Thu Jan 30 17:30:27 CET 2014
Thank you Bipin and Justin,
As far I understand from the very informative discussion, for A state (protonated) I will keep the charges and for B state (deprotonated) I will get them from the unprotonated GLU topology file and paste into this one .top file. The only difference will be the DUM atom which is the H to be transferred and it will have 0 charge.
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 Justin Lemkul <jalemkul at vt.edu>
Sent: Thursday, January 30, 2014 11:18 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] free energy calculations for reference state for constant pH MD simulations...
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.ozbil at 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-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: 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.ozbil at 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-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
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>>>>
>>>
>>>
>>>
>>> --
>>>
>>>
>>>
>>> *--------------------Thanks and Regards,Bipin Singh*
>>> --
>>> Gromacs Users mailing list
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>>
>>
>>
>> --
>>
>>
>>
>> *--------------------Thanks and Regards,Bipin Singh*
>> --
>> Gromacs Users mailing list
>>
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>
>
>
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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