[gmx-users] Restraining bilayer/water system

Xavier Periole x.periole at rug.nl
Fri Mar 17 12:32:13 CET 2006

Farid Sa'adedin wrote:

> Dear Xavier,
> My posre.itp file represents one lipid molecule.  My p1.itp represents 
> 1 water molecule.
> I made new itp files using genpr defining one lipid molecule and water 
> molecule called POSRE_L.itp and POSRE_W.itp as you suggested them to 
> be called.
> The strange thing is that I can restrain the lipids when there is no 
> water in my system.  But when I add water to the system, grompp 
> doesn't seem to restrain the lipids anymore.  It brings up this message:
>>> cpp exit code: 256
>>> cpp: too many input files
>>> [tripos]dopc/minidopc$ Tried to execute: '/lib/cpp -I 
>>> -I/usr/local/share/gromacs/top
>>> -DPOSRES dopc.top > grompptByAm1'
> [ system ]
> ; name
> DOPC in water
> #ifdef POSRES
> #include "/home/tripos/lipid/dopc/minidopc/POSRE_L.itp" in water
> ;#include "/home/tripos/lipid/dopc/minidopc/POSRE_W.itp" in water
> #endif

You should try to put this include at the end of the topology of your 
not here !!

define = -DPOSRES_L (-D)POSRES_W
you got to check if you need the second (-D), I never remember.

if you actually want to constraint the water !!

then call

#ifdef POSRES_L
#include "/home/tripos/lipid/dopc/minidopc/POSRE_L.itp"

#ifdef POSRES_W
#include "/home/tripos/lipid/dopc/minidopc/POSRE_W.itp"

you have a ; character at the beginning of the line !!

 Xavier Periole - Ph.D.

 Dept. of Biophysical Chemistry / MD Group   
 Univ. of Groningen
 Nijenborgh 4
 9747 AG Groningen
 The Netherlands
 Tel: +31-503634329
 Fax: +31-503634398
 email: x.periole at rug.nl
 web-page: http://md.chem.rug.nl/~periole

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