[gmx-users] Restraining bilayer/water system

[fsaadedi at staffmail.ed.ac.uk]

The posre itp file represents one lipid molecule and the p2.itp file 
represents all water molecules.
I have a p1.itp file that represents one water molecule but this also 
brought up the :

>> 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'
message.

TOP FILE:

#include "/home/tripos/lipid/ffgmx2_lipid.itp"
#include "/home/tripos/lipid/DOPCHT.itp"
#include "/usr/local/share/gromacs/top/spc.itp"


[ system ]
; name
DOPC in water

#ifdef POSRES
#include "/home/tripos/lipid/dopc/minidopc/posre.itp" in water
;#include "/home/tripos/lipid/dopc/minidopc/p2.itp" in water
#endif

[ molecules ]
; name number

DOPC    18



SOL              1463


Quoting Yang Ye <leafyoung81-group at yahoo.com>:

> You shall append those three lines just under the definition of the
> lipid molecule. You may paste your top file for us to comment.
>
> Yang Ye
>
> Farid Sa'adedin wrote:
>> Dear Users,
>>
>> I have been trying to equilibrate a bilayer.  I have been able to 
>> restrain a bilayer in its own system using
>>
>> #ifdef POSRES
>> #include "/home/tripos/lipid/dopc/minidopc/posre.itp"
>> #endif
>>
>> in the topology file
>>
>> define = -DPOSRES
>> in the steep, nvt and npt mdp files.
>>
>> The problem occurs when I add water to the system and for some 
>> reason when I just want to restrain the
>> the bilayer GROMACS doesn't recognise the posre.itp file even though 
>> it becomes in the top.
>>
>> #ifdef POSRES
>> #include "/home/tripos/lipid/dopc/minidopc/posre.itp" in water
>> #endif
>>
>> This is the line I get when I run grompp:
>>
>> 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'
>>
>> So as a result it doesn't restrain the lipids in the simulation.
>>
>>
>> If anyone has any ideas on how to just restrain a lipids with water 
>> in the system I would greatly appreciate them.
>>
>> Yours sincerely,
>>
>> Farid Sa'adedin--
>>
>>
>>
>> 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
>>
>>
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please don't post (un)subscribe requests to the list. Use the www 
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>