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

Justin Lemkul jalemkul at vt.edu
Thu Nov 2 17:12:50 CET 2017

On 11/2/17 12:05 PM, Hermann, Johannes wrote:
> Dear Justin, dear all,
> thank you for your reply. I will test the web server when I have 
> managed to generate the mol2 file for FMN.
> I had a look in the rtp file of charmm36 ff and I detected that there 
> are three "NADHs": NAD1 , NAI, and NAD1. NAI is the pdb 3 letter code 
> for the reduced form of NAD+ (https://www4.rcsb.org/ligand/NAI), i.e. 
> NADH. However, both NAI and NADH in the rtp file have only 71 atoms, 
> while they should have 73. Hence, if I am not mistaken, NAI and NADH 
> are both NAD (not NADH or NAD+).
> Has anyone who is reading this a ff field which he can send me? This 
> would save me a lot of time.

Anyone using the CHARMM force field should go to the MacKerell website 
and download the CHARMM-formatted topology and parameter files - they 
contain full chemical names and text drawings of structures. 
Unfortunately, there is no easy way to port all of this stuff to GROMACS 
so it gets lost. But if you ever need clarification, go to the source.

NAD1: oxidized NAD (so it is NAD+), net charge -1
NAI and NADH: reduced NAD (so it is NADH), net charge -2

I don't know the history of why there are both NAI and NADH residues.



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


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