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
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