[gmx-users] [Fwd: How simulate two peptides in a box?]

[David van der Spoel]

Mark Abraham wrote:
>> Thanks Mark for your advice
>>
>>  I tried to run the simulation even by removing all the restraints as you
>> told but the same problem was coming.
>> In your  second reply you asked me to check the topology file. I have a
>> doubt in that, actually what are the things i should look at in the
>> topology
>> file. I have seen my topology file and the related .itp files also but i
>> did
>> not find anything unusual in that.
>>
>> Following are the contents of my Topology file:
>>
>> ; Include forcefield parameters
>> #include "ffG43a1.itp"
>>
>> ; Include chain topologies
>> #include "aquapomut_grom_A.itp"
>> #include "aquapomut_grom_B.itp"
>>
>> ; Include water topology
>> #include "spce.itp"
>>
>> #ifdef POSRES_WATER
>> ; Position restraint for each water oxygen
>> [ position_restraints ]
>> ;  i funct       fcx        fcy        fcz
>>    1    1       1000       1000       1000
>> #endif
>>
>> ; Include generic topology for ions
>> #include "ions.itp"
>>
>> [ system ]
>> ; Name
>> Protein in water
>>
>> [ molecules ]
>> ; Compound        #mols
>> Protein_A           1
>> Protein_B           1
>> SOL                71
>> CL-                 6
>> SOL             14825
> 
> Two regions of SOL doesn't sound like a good idea, but I won't swear it's
> the problem.

this is why I suggested grompp -maxwarn 0, because it will detect the 
inconsistencies in names and tell you to fix it.


> 
> Mark
> 
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> 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


-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se