[gmx-users] protein membrane water simulations

[Weidong Xin]

Hi,
On Wed, 18 Jan 2006, Antonio Sergio Kimus Braz wrote:

> Hi all
>
>
>  I work in a molecular dynamic system : membrane carrier in a lipid bilayer
> (pope) + water
>
>
>  the protein was insert in pope lipid bilayer ...
>
>
>  but now I have problems with in execute *grompp*
>
>
>  I dowload e put correct :
>
>
>  pope.pdb and pope.itp
>
>
>  and Ii include the files
>
>
>  *lipid.itp, ffgmx.itp ffgmxnb.itp and ffgmxbon.itp*
>
>
>  I use gromacs 3.3 with (GROMOS96 43a1 force field)
>
>
>  My top file have :
>
>
>  ; Include forcefield parameters
> #include "ffG43a1.itp"
> and...
> ; topology for a pure POPE bilayer with 56 lipids and 8213 SPC water
> ; molecules
>
> #include "ffgmx.itp"
> #include "lipid.itp"
> #include "pope.itp"
>
> #ifdef FLEX_SPC
> #include "flexspc.itp"
> #else
> #include "spc.itp"
> #endif
>
>
>  and when i run grompp i have thsi message error
>
>
>
>  *Program grompp, VERSION 3.3*
>
> *Source code file: topio.c, line: 385*
>
>
>  *Fatal error:*
>
> *Invalid order for directive defaults, file ""ffgmx.itp"", line 4*
>
>
>
>  But I can not find error in this file in that line
>
>
>  ffgmx.itp :
>
>
>  *#define _FF_GROMACS**#define _FF_GROMACS1*
> *[ defaults ]**; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ*
>   *1             1               no              1.0     1.0*
> *#include "ffgmxnb.itp"**#include "ffgmxbon.itp"*
>
> the error is line 4 : [ defaults ]
>
>
>
>
>
>  Some one can help me ?
>
>
>  Thanks !
>
>
>  Antonio Sérgio Kimus Braz
>
You should include the definition of your *protein
molecule* (Protein) in .top file.

with BR,
Weidoong