On 10/30/17 10:58 AM, Hermann, Johannes wrote:
Dear all,
I want to simulate a complex consisting of a protein, FMN, and NADH. I
have two problems/questions:
1) In the "CHARMM36 all-atom force field (March 2017)" parameters for
NADH are present. But apparently I am using a wrong atom naming
convention (I copied / pasted NADH from a pdb entry):
Fatal error:
Atom PN in residue NADH 0 was not found in rtp entry NADH with 71 atoms
while sorting atoms.
How can I generate a appropriate input file for gromacs gmx2pdb?
Make the PDB file atom names match those of the .rtp entry. It's a bit
awkward but everyone seems to have a different convention for naming
cofactor atoms.
2) I did not find FMN in the charmm36 force field. Can some recommend
me a program to generate a parameter file? And how to proceed with it?
If it's not in CHARMM, use CGenFF. There's a web server that will
parametrize it (cgenff.paramchem.org) and tell you how good the topology
is so you can decide if you need to do any manual parametrization.
Download the .str -> .itp conversion script from the MacKerell lab
webpage and you're ready for GROMACS.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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