Thanks a lot........now it's working....:) On Fri, Jun 15, 2012 at 2:00 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote:
> On 15/06/2012 6:21 PM, tarak karmakar wrote: > > Hi, > > Thanks for the reply. > One thing, while giving the '-ff' flag it is asking for some string. So I > renamed all my force field files as except spc.itp and ions.itp. Renamed > files are ..... > > 1) ffprot.atp > 2) ffprot.rtp > 3) ffprot.itp [ includes ffnonbonded.itp and ffbonded.itp ] > > pdb2gmx -f test.pdb -o test.gro -p toplo.top -ff prot > > so it'll read all of these files starting with 'ff' > Then how can I deal with spc.itp and ions.itp files ?? Should I include > the scp.itp and ions.itp files inside the ffprot,itp ?? > > On Fri, Jun 15, 2012 at 12:50 PM, Mark Abraham > <mark.abra...@anu.edu.au>wrote: > >> >> You need the kind of approach described here >> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field >> >> > You started with files from some force field. Copy the whole folder, like > it says in the above link. Then modify the files there... > > Mark > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- *Tarak Karmakar Molecular Simulation Lab. Chemistry and Physics of Materials Unit Jawaharlal Nehru Centre for Advanced Scientific Research Jakkur P. O. Bangalore - 560 064 Karnataka, INDIA Ph. (lab) : +91-80-22082809 *
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