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

[Justin Lemkul]

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

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

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