P.R.Anand Narayanan wrote:
dear gromacs users,
my protein has a cofactor FAD, and NAG sugar along with it. these are
present in the protein's PDB file itself.
while creating the topology, are we supposed to add FAD's and NAG's itp
under
"Include forcefield parameters" by downloading it separately and also
should I add the molecules name and number under
";Compound #mols"
Refer to chapter 5 in the manual. I don't know what you mean by "downloading it
separately," but you do need to account for all species in your system through
the appropriate use of #include and listing of molecules.
-Justin
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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