[gmx-users] simulation popc

[mahbubeh zarrabi]

Dear yang
thanks very much.the some of atomes do not
found(NR,CH,N5,...).they are in lipid.itp
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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> 
> 
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