[gmx-users] Restraining bilayer/water system

[Xavier Periole]

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'
>>
>
> TOP FILE:
>
> [ 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 
lipid.itp.
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"
#endif

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

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
----------------------------------