[gmx-users] Restraining bilayer/water system

[fsaadedi at staffmail.ed.ac.uk]

Dear Xavier,

I have put the posre.itp file in the order that you mentioned and I 
have a file which has postional restraints on one water molecule.
(See previous email below)  So it is not an ordering problem.

If anyone has any suggestions why grompp isn't restraining just the 
lipid molecules in my bilayer/water system I would greatly appreciate 
it.


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 Xavier Periole <x.periole at rug.nl>:

> fsaadedi at staffmail.ed.ac.uk wrote:
>
>>
>> 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'
>>>
> You have to be very carefull in the order that you include the
> information into the
> topology files.
> Basically you should include the information of posre after tohe
> topology with the
> "ifdef" flag ...
>
> AND the position restrain on water must not include all water molecules !
> You define it for one molecule.
>
> XAvier
>
> -- 
> ----------------------------------
>  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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