[gmx-users] Restraining bilayer/water system

[Yang Ye]

attach your top to the list? or just send to me directly.

Yang Ye

Farid Sa'adedin wrote:
> 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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>