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
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