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

[Hermann, Johannes]

Dear Justin,

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 : 
3.0.1

BUT: NAI is only present in charmm36-jul2017 ff, which uses CGenFF 
version 4.0

   --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
Johannes

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 
> 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
>

-- 
______________________________________
*Technische Universität München*
*Johannes Hermann, M.Sc.*
Lehrstuhl für Bioverfahrenstechnik
Boltzmannstr. 15
D-85748 Garching
Tel: +49 8928915730
Fax: +49 8928915714

Email: j.hermann at lrz.tum.de
http://www.biovt.mw.tum.de/