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On 15/06/2012 4:27 PM, tarak karmakar wrote:
<blockquote
cite="mid:CAGZMOovxVoO3YY5qfgt269aKVyYtngXFLfWNu3BeuPSxuzqqdg@mail.gmail.com"
type="cite"><font size="4">Dear All,<br>
<br>
<br>
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 <br>
<br>
1) atomtypes.atp<br>
2) aminoacids.rtp<br>
3) ffnonbonded.itp<br>
4) ffbonded.itp<br>
5) spc.itp<br>
6) ions.itp<br>
<br>
now while giving the command <br>
pdb2gmx -f prot.pdb -o prot.gro -p toplogy.top <br>
<br>
how can I make use of all these force field files present in my
current working directory ?</font><br>
</blockquote>
<br>
You need the kind of approach described here <a
href="http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field">http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field</a><br>
<br>
Mark<br>
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