[gmx-users] force field / parameters for NADH, FMN
J.Hermann at lrz.tu-muenchen.de
Fri Nov 3 15:34:02 CET 2017
thanks - again - for your reply!
Now I get duplicated parameters warnings and errors:
WARNING 1 [file fmn.prm, line 5]:
Overriding Bond parameters.
old: 0.1295 405848 0.1295
new: CG2R64 NG2D1 1 0.14140000 255224.00
ERROR 1 [file fmn.prm, line 35]:
Encountered a second block of parameters for dihedral type 9 for the same
atoms, with either different parameters and/or the first block has
multiple lines. This is not supported.
I did *not* tick the "Include parameters that are already in CGenFF" on
the webserver when generating the str file. I am using the newest
version of cgenff_charmm2gmx.py. Do you have any hint for me?
Thanks in advance!
All the best
On 03.11.2017 13:18, Justin Lemkul wrote:
> 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.
*Technische Universität München*
*Johannes Hermann, M.Sc.*
Lehrstuhl für Bioverfahrenstechnik
Tel: +49 8928915730
Fax: +49 8928915714
Email: j.hermann at lrz.tum.de
More information about the gromacs.org_gmx-users