[gmx-users] free energy calculations for reference state for constant pH MD simulations...
Ozbil, Mehmet
m.ozbil at umiami.edu
Thu Jan 30 19:37:04 CET 2014
I think so, because when I try to run grompp to create a .tpr file for the steepest descent energy minimization it gave me these following three WARNINGS:
Generated 333336 of the 333336 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 333336 of the 333336 1-4 parameter combinations
WARNING 1 [file GLUA_prot_OPLS_p.top, line 64]:
No default Bond types for perturbed atoms, using normal values
WARNING 2 [file GLUA_prot_OPLS_p.top, line 138]:
No default Angle types for perturbed atoms, using normal values
WARNING 3 [file GLUA_prot_OPLS_p.top, line 152]:
Some parameters for bonded interaction involving perturbed atoms are
specified explicitly in state A, but not B - copying A to B
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
turning H bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning H bonds into constraints...
Coupling 1 copies of molecule type 'Protein_chain_A'
Can you tell me what shall I do, to change the corresponding pairs and dihedrals for the two states?
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: Thursday, January 30, 2014 12:19 PM
To: Discussion list for GROMACS users; Justin Lemkul
Subject: Re: [gmx-users] free energy calculations for reference state for constant pH MD simulations...
I think the corresponding dihedral (involving the HE2 atom) also need to be
changed in the B state during the transformation.
On Thu, Jan 30, 2014 at 9:48 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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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>>>>> posting!
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>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>>
>>>>
>>>>
>>>> *--------------------Thanks and Regards,Bipin Singh*
>>>> --
>>>> Gromacs Users mailing list
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>>>
>>>
>>> --
>>>
>>>
>>>
>>> *--------------------Thanks and Regards,Bipin Singh*
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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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