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

Justin Lemkul jalemkul at vt.edu
Fri Nov 3 13:18:50 CET 2017

On 11/3/17 8:17 AM, Hermann, Johannes wrote:
> 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?

Ignore it. The differences between the two are not relevant here. It has 
taken an unfortunately long time to get the CGenFF server updated and I 
don't know when it will happen.



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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