Hey Justin,
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
405848
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
Johannes
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.
-Justin
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*Johannes Hermann, M.Sc.*
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Email: j.herm...@lrz.tum.de
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