[gmx-users] Restraining bilayer/water system

[Farid Sa'adedin]

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
  -I/usr/local/share/gromacs/top
-DPOSRES_L dopc.top > grompptByAm1'

Any other ideas would be greatly appreciated.

Farid

Farid Sa'adedin
Membrane Biophysics Laboratory
Department of Veterinary Biomedical Sciences
College of Medicine & Veterinary Medicine
Royal (Dick) School of Veterinary Studies
University of Edinburgh
Summerhall
Edinburgh EH9 1QH
SCOTLAND


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 
>> 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
> ----------------------------------
>
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