Dear all,
I have been playing with parmed to get some ff parameters, in particular
the dihedral angles of O-C-N-CX and CX-C-N-H. I have three questions:
1. I have been looking in frcmod.ff114SB and parm10.dat files (I am
using leaprc.ff14SB) the aforementioned dihedral angles but I could not
find them. I suppose it is this one:
X -C -N -X 4 10.00 180.0 2. AA,NMA
right?
2. using parmed to get the aforementioned dihedral angles:
(.O.C.N.H)&:1|:2
give me back several results. How can I get *only" the info on O-C-N-H?
3. tleap is complaining about a dihedral angles missing on my ligand.
Unexpectedly, just adding the dihedral angles in the frcmod file as
following
O-C-N-CX
without values, tleap was able to generate the topology. Could you
explain why it is enough to add the string without values to make tleap
happy?
Best
and
--
Andrea Spitaleri PhD
Computational mOdelling of NanosCalE and bioPhysical sysTems - CONCEPT Lab
ISTITUTO ITALIANO DI TECNOLOGIA
Via Morego 30, 16163 - Genova, Italy
https://iit.it/research/lines/computational-modelling-of-nanoscale-and-biophysical-systems
cell: +39 3485188790
https://iit.it/andrea-spitaleri
ORCID: http://orcid.org/0000-0003-3012-3557
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Received on Fri May 05 2017 - 01:00:03 PDT
