[gmx-users] Regarding cofactors

Justin A. Lemkul jalemkul at vt.edu
Mon Jul 13 13:30:13 CEST 2009

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.


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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


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