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: > On 15/06/2012 4:27 PM, tarak karmakar wrote: > > Dear All, > > > In my protein pdb file I have changed some of the amino acid residue > names. So accordingly I have changed corresponding residue names in force > filed files and kept all the files [ modified and unmodified ] in my > current working directory. Those files are > > 1) atomtypes.atp > 2) aminoacids.rtp > 3) ffnonbonded.itp > 4) ffbonded.itp > 5) spc.itp > 6) ions.itp > > now while giving the command > pdb2gmx -f prot.pdb -o prot.gro -p toplogy.top > > how can I make use of all these force field files present in my current > working directory ? > > > You need the kind of approach described here > http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field > > 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 *
-- 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
