[gmx-users] force field / parameters for NADH, FMN

Justin Lemkul jalemkul at vt.edu
Mon Oct 30 16:14:43 CET 2017

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 A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


More information about the gromacs.org_gmx-users mailing list