[gmx-users] simulation popc

[Yang Ye]

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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