[gmx-users] Restraining bilayer/water system

[Farid Sa'adedin]

Dear Yang Ye,

Apologies for the late reply.

Here is my top file:

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_L
#include "/home/tripos/lipid/dopc/minidopc/POSRE_L.itp" in water
#endif

[ molecules ]
; name number

DOPC    18



SOL              1463

In my mdp files I specified under preprocessing:

define  = -DPOSRES_L

but I still obtain this message 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_L dopc.top > grompptByAm1'


Thank you for allowing me to send you the top.

Yours sincerely,

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

> 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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>>
>
>
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