[gmx-users] simulation popc
Tsjerk Wassenaar
tsjerkw at gmail.com
Thu Jun 14 10:43:03 CEST 2007
Hi Jordi et al.
Note the ffgmx force field should not be used for production runs. The
force field is deprecated. Check the archives for more discussion on
that. To use popc in simulation, try to dig up popc parameters for a
current force field (like ffG43a1).
Tsjerk
On 6/12/07, Jordi Camps <jcamps at lsi.upc.edu> wrote:
> I think I arrive a little late, but I will try to help :-)
>
> I think I get the meaning.
> It sounds me like you are generating the protein topology for the G43a1
> force field (or some one different than ffgmx). Try generating the
> protein topology for the gmx force field. Then the atom names will be
> defined.
>
> Jordi Camps Puchades
> jcamps at lsi.upc.edu
> Supercomputing research, support and development
>
> Barcelona Supercomputing Center | Instituto Nacional de Bioinformática
> | GNHC-2 UPC-CIRI
> (http://inb.lsi.upc.edu)
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> Fax : 934 137 721 | Fax : 934 037 157
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>
> Yang Ye escribió:
> > On 5/28/2007 9:23 PM, mahbubeh zarrabi wrote:
> >> Dear yang
> >> thanks very much.the some of atomes do not
> >> found(NR,CH,N5,...).they are in lipid.itp
> >>
> > Didn't get what you mean? Any other problems?
> >
> > Regards,
> > Yang Ye
> >> best wishes
> >> --- Yang Ye <leafyoung at yahoo.com> wrote:
> >>
> >>
> >>> You shall read up manual for the structure of
> >>> topology file.
> >>>
> >>> For your problem, you shall create a top file which
> >>> contains
> >>>
> >>> #include "ffgmx.itp"
> >>> #include "lipid.itp"
> >>> #include "popc.itp"
> >>> #include "prox.itp"
> >>> #ifdef POSRES
> >>> ; #include "prox-posre-100000.itp"
> >>> #include "prox-posre.itp"
> >>> #endif
> >>> #include "spc.itp"
> >>> #ifdef POSRES_WATER
> >>> ; Position restraint for each water oxygen
> >>> [ position_restraints ]
> >>> ; i funct fcx fcy fcz
> >>> 1 1 1000 1000 1000
> >>> #endif
> >>> ; Include generic topology for ions
> >>> #include "ions.itp"
> >>> [ system ]
> >>> ; Name
> >>> protein and POPC
> >>> [ molecules ]
> >>> ; Compound #mols
> >>> Protein_X 1
> >>> POP 489
> >>>
> >>> Regards,
> >>> Yang Ye
> >>>
> >>> ----- Original Message ----
> >>> From: mahbubeh zarrabi <zarrab_m at yahoo.com>
> >>> To: Yang Ye <leafyoung at yahoo.com>; Discussion list
> >>> for GROMACS users <gmx-users at gromacs.org>
> >>> Sent: Monday, May 28, 2007 7:56:23 PM
> >>> Subject: Re: [gmx-users] simulation popc
> >>>
> >>>
> >>> dear freind
> >>> thanks for helping. there is another errore: no such
> >>> moleculetype protein.
> >>> best wishes
> >>> --- Yang Ye <leafyoung at yahoo.com> wrote:
> >>>
> >>>
> >>>> Put two semicolon before
> >>>>
> >>>> ;[ defaults ]
> >>>> ;1 1
> >>>>
> >>>> in the lipid.itp
> >>>>
> >>>> ----- Original Message ----
> >>>> From: mahbubeh zarrabi <zarrab_m at yahoo.com>
> >>>> To: gmx-users at gromacs.org
> >>>> Sent: Monday, May 28, 2007 4:41:19 PM
> >>>> Subject: [gmx-users] simulation popc
> >>>>
> >>>>
> >>>> Dear all
> >>>> I want to simulate protein in popc.I dowanload
> >>>> popc128a.pdb from tieleman site and insert protein
> >>>> in
> >>>> popc by VMD BUT I can not run grompp.there is
> >>>> errore:
> >>>> found a second defaults directive file ffgmx.itp
> >>>> line6.whould you please help me?which protocole is
> >>>> useful for me(in detail)?
> >>>> best regard
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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