[gmx-users] Restraining bilayer/water system
fsaadedi at staffmail.ed.ac.uk
Fri Mar 17 13:40:02 CET 2006
Dear Xavier and Yang Ye,
I have done what you suggested by adding it to the lipid itp and
modifying the mdp files, but I still get the same message
cpp exit code: 256
cpp: too many input files
[tripos]dopc/minidopc$ Tried to execute: '/lib/cpp -I
-DPOSRES_L dopc.top > grompptByAm1'
Any other ideas would be greatly appreciated.
Membrane Biophysics Laboratory
Department of Veterinary Biomedical Sciences
College of Medicine & Veterinary Medicine
Royal (Dick) School of Veterinary Studies
University of Edinburgh
Edinburgh EH9 1QH
Quoting Xavier Periole <x.periole at rug.nl>:
> 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
>>>> cpp exit code: 256
>>>> cpp: too many input files
>>>> [tripos]dopc/minidopc$ Tried to execute: '/lib/cpp -I
>>>> -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
> 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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