[AMBER] AMBER atom types in parm10.dat don't match antechamber

From: Brian Radak <radak004.umn.edu>
Date: Mon, 1 Jul 2013 10:50:13 -0400

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

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.

================================ 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
 radak004.umn.edu                                 :
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Received on Mon Jul 01 2013 - 08:00:04 PDT
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