I'm running calculations on a bunch of nucleic acids and analogues. Since
these are non-standard non-nucleobase compounds I used antechamber to
assign atom types. However, it would appear that the hydrogen Lennard-Jones
parameters for atoms of the same type do not match in prmtops generated
from antechamber files and those from leaprc.ff10
(using parmed.py printDetails)
Rmin/2 epsilon
type AC FF10 AC FF10
H4 1.4870 1.4090 0.0157 0.0150
HA 1.4870 1.4590 0.0157 0.0150
the AC parameters were obtained by starting with a simple pdb (no atom
types):
antechamber -i <pdbname> -fi pdb -o <mol2name> -fo mol2 -at amber -c bcc -s
2 -nc 0
parmchk -i <mol2name> -f mol2 -o <frcmodname>
and the following tleap script:
source leaprc.ff10
loadamberparams <frcmodname>
MOL = loadmol2 <mol2name>
saveamberparm MOL <prm7> <rst7>
I'm guessing I messed something up here by reloading parameters. Should I
not be creating a new frcmod? Still, I find it weird that two atoms would
have the same type but different parameters. Where does the flag "-at
amber" get parameters from? I assumed these would be the same LJ types that
have been around since FF94.
Thanks,
Brian
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Mon Jul 01 2013 - 08:00:04 PDT
