[gmx-users] protein membrane water simulations
Weidong Xin
xin at sun3.oulu.fi
Thu Jan 19 07:50:31 CET 2006
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
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