[gmx-users] force field / parameters for NADH, FMN
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
> 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 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.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
More information about the gromacs.org_gmx-users