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