[gmx-users] force field / parameters for NADH, FMN
J.Hermann at lrz.tu-muenchen.de
Fri Nov 3 13:17:06 CET 2017
thanks for the hint with the CHARMM-formatted topology and parameter
files! That is great help! I had a different atom number compared to NAI
and NADH because I had a different (non-physical) protonation state. The
text drawing helped me a lot to figure out the few Nomenclature
differences between my pdb and the NAI in rtp file.
For my other coenzyme, Flavin mononucleotide (FMN), I got the mol2 file
from the ZINC Database and applied cgenff.paramchem.org and converted it
with your python script (cgenff_charmm2gmx.py) to Gromacs format.
I now have the following issue:
The CGenFF version on the webserver is 3.0.1
NOTE2: Please be sure to use the same version of CGenFF in your
simulations that was used during parameter generation:
--Version of CGenFF detected in fmn.str : 3.0.1
Therefore, I should use the charmm36-nov2016 ff:
--Version of CGenFF detected in charmm36-nov2016.ff/forcefield.doc :
BUT: NAI is only present in charmm36-jul2017 ff, which uses CGenFF
--Version of CGenFF detected in charmm36-jul2017.ff/forcefield.doc : 4.0
Do you have any suggestion on how I could resolve this issue?
Thank you very much in advance!
All the best
On 02.11.2017 17:12, Justin Lemkul wrote:
> 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
> 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.
*Technische Universität München*
*Johannes Hermann, M.Sc.*
Lehrstuhl für Bioverfahrenstechnik
Tel: +49 8928915730
Fax: +49 8928915714
Email: j.hermann at lrz.tum.de
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