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

From: David A Case <>
Date: Mon, 1 Jul 2013 21:54:19 -0400

On Mon, Jul 01, 2013, Brian Radak wrote:

> 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 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
> 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.

I think this is one of those cases where Junmei tried to make antechamber do
too many things. Some features are very rarely used, and results may have
diverged over the years.

The files in question are ATOMTYPE_AMBER.DEF and PARMCHK.DAT (both in
$AMBERHOME/dat/antehcamber.) If I read your email correctly, you are getting
OK atom types, but parmchk is giving odd LJ parameters. That's pretty easy to
work around. It's always recommended to use antechamber as a starting point,
but this is especially true when trying to get it to spit out Amber atom
types: be sure to examine what comes out carefully.

(Also note the hydrogens have notorious fickle LJ parameters, especially in
"Amber" force fields.)


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Received on Mon Jul 01 2013 - 19:00:04 PDT
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