Hi Justin,
just for testing, I applied cgenff_charmm2gmx.py with
charmm36-nov2016.ff as it has the same CGenFF version:
--Version of CGenFF detected in
/usr/local/gromacs/share/gromacs/top/charmm36-nov2016.ff/forcefield.doc
: 3.0.1
But I still get the same warnings and errors.
Would you
On 11/3/17 10:33 AM, Hermann, Johannes wrote:
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
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 0.1414
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
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
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.
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
On 10/30/17 10:58 AM, Hermann, Johannes wrote:
Dear all,
I want to simulate a complex consisting of a protein, FMN, and NADH. I
have two problems/questions:
1) In the "CHARMM36 all-atom force field (March 2017)" parameters for
NADH are present. But apparently I am using a wrong atom
Dear all,
I want to simulate a complex consisting of a protein, FMN, and NADH. I
have two problems/questions:
1) In the "CHARMM36 all-atom force field (March 2017)" parameters for
NADH are present. But apparently I am using a wrong atom naming
convention (I copied / pasted NADH from a pdb
