[gmx-users] Re: gmx-users Digest, Vol 79, Issue 114
ITHAYARAJA
ithayaraja at gmail.com
Tue Nov 16 11:40:01 CET 2010
Dear Sir,
Greetings!
It may be basic question but it is very important to go further, my doubt
is,
My protein is soluble form with three ligand and two of them are hetatm (FAD
and NADPH) i would like study the substrate, hetatm ligand simulation by
gromacs. please make clear to understand and how to do my hetatm to pdb file
Thanks in advance
On 16 November 2010 04:03, <gmx-users-request at gromacs.org> wrote:
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> Today's Topics:
>
> 1. Protein in Electric Field (S. Mohamadi)
> 2. Re: Re: still can not run md for creatine
> (Esteban Gabriel Vega Hissi)
> 3. Re: Protein in Electric Field (Mark Abraham)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 16 Nov 2010 07:54:52 +0330
> From: "S. Mohamadi" <samira.0630 at gmail.com>
> Subject: [gmx-users] Protein in Electric Field
> To: gmx-users at gromacs.org
> Message-ID:
> <AANLkTikZFpqCGsk-g17Zo+3+6t4s1ed3K2gYcpAsN97M at mail.gmail.com<AANLkTikZFpqCGsk-g17Zo%2B3%2B6t4s1ed3K2gYcpAsN97M at mail.gmail.com>
> >
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear All
>
>
> I want to simulate a protein in Electric Field how can I do that? where
> should I start from!
> It's very Important for me! Please help me!
>
> Thanks
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> Message: 2
> Date: Tue, 16 Nov 2010 03:47:54 -0300
> From: Esteban Gabriel Vega Hissi <egvega at gmail.com>
> Subject: Re: [gmx-users] Re: still can not run md for creatine
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <AANLkTinqkL_MC+vdCENYceKZYQW3EeSLkz7f3RZzPGiy at mail.gmail.com<AANLkTinqkL_MC%2BvdCENYceKZYQW3EeSLkz7f3RZzPGiy at mail.gmail.com>
> >
> Content-Type: text/plain; charset="iso-8859-1"
>
> Justin,
>
> Regarding the charges you mention, what do you think about RESP charges for
> this kind of compounds (drugs) parameterization?
>
> Best wishes
>
> Esteban
>
> --
> On Mon, Nov 15, 2010 at 11:12 PM, Justin A. Lemkul <jalemkul at vt.edu>
> wrote:
>
> >
> > Just the $0.02 that I always seem to contribute in these types of
> > discussions - the topology you have shown below contains some likely
> > problems. The charges (and massive charge group size) can lead to
> > artifacts. We've got a paper due out soon about the implications of
> > incorrect charges, but I would advise you that this topology should *not*
> be
> > used for production simulation. You'd be better off spending the time to
> > properly parameterize the molecule rather than run a bunch of simulations
> > and get questionable (at best) or wrong (at worst) results.
> >
> > http://www.gromacs.org/Documentation/How-tos/Parameterization
> >
> > -Justin
> >
> > Olga Ivchenko wrote:
> >
> >>
> >> Hey Vitaly,
> >>
> >> Thank you for your reply. Here is the files:
> >>
> >> *itp:*
> >> ; ; ; This file was generated by PRODRG version
> >> AA081006.0504
> >> ; PRODRG written/copyrighted by Daan van Aalten
> >> ; and Alexander Schuettelkopf
> >> ; ; Questions/comments to dava at davapc1.bioch.dundee.ac.uk
> <mailto:
> >> dava at davapc1.bioch.dundee.ac.uk>
> >>
> >> ; ; When using this software in a publication, cite:
> >> ; A. W. Schuettelkopf and D. M. F. van Aalten (2004).
> >> ; PRODRG - a tool for high-throughput crystallography
> >> ; of protein-ligand complexes.
> >> ; Acta Crystallogr. D60, 1355--1363.
> >> ; ;
> >> [ moleculetype ]
> >> Name nrexcl
> >> DRG 3
> >>
> >> [ atoms ]
> >> ; nr type resnr resid atom cgnr charge mass
> >> 1 OM 1 DRG OXT 1 -0.701 15.9994 2
> >> C 1 DRG C 1 0.402 12.0110 3 OM 1
> DRG
> >> O 1 -0.701 15.9994 4 CH2 1 DRG CA 2
> >> 0.185 14.0270 5 N 1 DRG N 2 0.468
> 14.0067
> >> 6 CH3 1 DRG CAG 2 0.201 15.0350 7
> >> C 1 DRG CAH 2 0.377 12.0110 8 NZ 1
> DRG
> >> NAE 2 -0.163 14.0067 9 H 1 DRG HA6 2
> >> 0.023 1.0080 10 H 1 DRG HAE 2 0.024
> 1.0080
> >> 11 NZ 1 DRG NAD 2 -0.163 14.0067 12
> >> H 1 DRG HA5 2 0.024 1.0080 13 H 1
> DRG
> >> HAD 2 0.024 1.0080
> >> [ bonds ]
> >> ; ai aj fu c0, c1, ...
> >> 2 1 2 0.125 13400000.0 0.125 13400000.0 ; C OXT 2
> >> 3 2 0.125 13400000.0 0.125 13400000.0 ; C O 2 4
> 2
> >> 0.153 7150000.0 0.153 7150000.0 ; C CA 5 4 2
> 0.147
> >> 8710000.0 0.147 8710000.0 ; N CA 5 6 2 0.147
> >> 8710000.0 0.147 8710000.0 ; N CAG 5 7 2 0.134
> >> 10500000.0 0.134 10500000.0 ; N CAH 7 8 2 0.134
> >> 10500000.0 0.134 10500000.0 ; CAH NAE 7 11 2 0.134
> >> 10500000.0 0.134 10500000.0 ; CAH NAD 8 9 2 0.100
> >> 18700000.0 0.100 18700000.0 ; NAE HA6 8 10 2 0.100
> >> 18700000.0 0.100 18700000.0 ; NAE HAE 11 12 2 0.100
> >> 18700000.0 0.100 18700000.0 ; NAD HA5 11 13 2 0.100
> >> 18700000.0 0.100 18700000.0 ; NAD HAD
> >> [ pairs ]
> >> ; ai aj fu c0, c1, ...
> >> 1 5 1 ; OXT N 2
> >> 6 1 ; C CAG 2 7
> 1
> >> ; C CAH 3 5 1
> >> ; O N 4 8 1
> >> ; CA NAE 4 11 1
> >> ; CA NAD 5 9 1
> >> ; N HA6 5 10 1
> >> ; N HAE 5 12 1 ;
> N
> >> HA5 5 13 1 ; N
> HAD
> >> 6 8 1 ; CAG NAE 6
> 11
> >> 1 ; CAG NAD 8 12 1
> >> ; NAE HA5 8 13 1
> >> ; NAE HAD 9 11 1
> >> ; HA6 NAD 10 11 1
> >> ; HAE NAD
> >> [ angles ]
> >> ; ai aj ak fu c0, c1, ...
> >> 1 2 3 2 126.0 770.0 126.0 770.0 ; OXT C
> >> O 1 2 4 2 117.0 635.0 117.0 635.0 ; OXT
> C
> >> CA 3 2 4 2 117.0 635.0 117.0 635.0 ; O
> >> C CA 2 4 5 2 109.5 520.0 109.5 520.0 ;
> C
> >> CA N 4 5 6 2 121.0 685.0 121.0 685.0 ;
> >> CA N CAG 4 5 7 2 122.0 700.0 122.0
> 700.0 ;
> >> CA N CAH 6 5 7 2 117.0 635.0 117.0
> 635.0
> >> ; CAG N CAH 5 7 8 2 120.0 670.0 120.0
> >> 670.0 ; N CAH NAE 5 7 11 2 120.0 670.0 120.0
> >> 670.0 ; N CAH NAD 8 7 11 2 120.0 670.0
> 120.0
> >> 670.0 ; NAE CAH NAD 7 8 9 2 120.0 390.0
> 120.0
> >> 390.0 ; CAH NAE HA6 7 8 10 2 120.0 390.0
> >> 120.0 390.0 ; CAH NAE HAE 9 8 10 2 120.0
> 445.0
> >> 120.0 445.0 ; HA6 NAE HAE 7 11 12 2 120.0
> >> 390.0 120.0 390.0 ; CAH NAD HA5 7 11 13 2 120.0
> >> 390.0 120.0 390.0 ; CAH NAD HAD 12 11 13 2
> 120.0
> >> 445.0 120.0 445.0 ; HA5 NAD HAD
> >> [ dihedrals ]
> >> ; ai aj ak al fu c0, c1, m, ...
> >> 2 1 3 4 2 0.0 167.4 0.0 167.4 ; imp C OXT
> >> O CA 5 4 6 7 2 0.0 167.4 0.0 167.4 ; imp
> >> N CA CAG CAH 7 5 8 11 2 0.0 167.4 0.0 167.4
> ;
> >> imp CAH N NAE NAD 8 7 10 9 2 0.0 167.4
> 0.0
> >> 167.4 ; imp NAE CAH HAE HA6 11 7 13 12 2 0.0
> 167.4
> >> 0.0 167.4 ; imp NAD CAH HAD HA5 5 4 2 1 1
> 0.0
> >> 1.0 6 0.0 1.0 6 ; dih N CA C OXT 2 4 5 7
> 1
> >> 180.0 1.0 6 180.0 1.0 6 ; dih C CA N CAH 11 7
> 5
> >> 4 1 180.0 33.5 2 180.0 33.5 2 ; dih NAD CAH N CA
> 5
> >> 7 8 10 1 180.0 33.5 2 180.0 33.5 2 ; dih N CAH
> NAE
> >> HAE 5 7 11 13 1 180.0 33.5 2 180.0 33.5 2 ; dih
> N
> >> CAH NAD HAD
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> *And top. I am prettu sure this file is wrong. And I do not know yet how
> >> to modify it correctly:
> >>
> >> *
> >>
> >> ;
> >> ; File 'creatine.top' was generated
> >> ; By user: onbekend (0)
> >> ; On host: onbekend
> >> ; At date: Mon Nov 15 13:24:44 2010
> >> ;
> >> ; This is your topology file
> >> ; it was generated using program:
> >> ; pdb2gmx - version 4.5-beta2
> >> ; with command line:
> >> ; pdb2gmx -f creatine_all_hyd_PRODRGBeta.pdb -o creatine.gro -p
> >> creatine.top
> >> ;
> >>
> >> #include "creatine.itp"
> >> #include "gromos43a1.ff"
> >>
> >>
> >> ; Include forcefield parameters
> >> ;#include "gromos43a1.ff/forcefield.itp"
> >>
> >> ;"gromos43a1.ff/creatine.itp"
> >>
> >>
> >> ;[ system ]
> >>
> >> ;[ molecules ]
> >> ;DRG 3
> >>
> >>
> >>
> >>
> >> 2010/11/15 Vitaly Chaban <vvchaban at gmail.com <mailto:vvchaban at gmail.com
> >>
> >>
> >>
> >> Hey, Olga -
> >>
> >> > Also please can you tell me where can I get "ffgmx.itp" file?
> >>
> >> /$gromacs_folder/share/gromacs/top/ffgmx.itp as well as all other
> >> standard topology files are there.
> >>
> >> By trying to run md I am getting an error: Fatal error:
> >> > moleculetype UNK is redefined
> >>
> >> Please post you top and itp files here. Looks like you have 2
> creatine
> >> molecules in your topology right now.
> >>
> >> Good luck!
> >>
> >> Vitaly
> >>
> >>
> >>
> >>
> >> > I still have troubles of starting running md for creatine. For
> >> which I
> >> > created topology using PRODRG programm.
> >> > The only difference between creatine.top and creating.itp is that
> >> creatine
> >> > top has additional lines:
> >> > #include "ffgmx.itp"
> >> > #include "creatine.itp"
> >> >
> >> > Also please can you tell me where can I get "ffgmx.itp" file?
> >> >
> >> > By trying to run md I am getting an error: Fatal error:
> >> > moleculetype UNK is redefined
> >>
> >>
> >>
> > --
> > ========================================
> >
> > Justin A. Lemkul
> > Ph.D. Candidate
> > ICTAS Doctoral Scholar
> > MILES-IGERT Trainee
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > ========================================
> >
> > --
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> Message: 3
> Date: Tue, 16 Nov 2010 20:03:03 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Protein in Electric Field
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4CE248C7.7020103 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> On 16/11/2010 3:24 PM, S. Mohamadi wrote:
> > Dear All
> >
> >
> > I want to simulate a protein in Electric Field how can I do that?
> > where should I start from!
> > It's very Important for me! Please help me!
> >
> > Thanks
>
> Start by looking in the manual.
>
> Mark
>
>
> ------------------------------
>
> --
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> End of gmx-users Digest, Vol 79, Issue 114
> ******************************************
>
--
--
*With love and gratitude of,*
Ithayaraja M,
Research Scholar,
Department of Bionformatics,
Bharathiar University,
Coimbatore 641 046,
Tamil Nadu
India
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