AMBER Archive (2009)

Subject: Re: [AMBER] specification of antechamber AC file format?

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Thu Apr 16 2009 - 07:29:46 CDT

On Wed, Apr 15, 2009, Nicholas Musolino wrote:

> 1) Does parmchk require GAFF atomtypes? Or another atomtype format?

Yes. It won't work with sybyl atom types, as you have discoverd.

> 3) Do the atom names (field 2) need to be different for each atom, e.g.
> H1, H2, ... H10?

This is needed for Amber, not sure about parmchk itself. Antechamber
will create unique atom names if needed, but they may not make any
chemical sense.

>
> More generally, I am able to produce MOL2 files of arbitrary molecules
> with (a) SYBYL atom type information and (b) bond information that I
> deem trustworthy. What is the best way to obtain an FRCMOD file, and
> then a PARM7 file, for later use with NAMD?

The fact that you have sybyl atom types you like is not going to help
much. Amber/antehcamber doesn't deal with the sybyl force field. As
for the bonds, play with the "-j" flag for your problem molecules to see
if that helps. If you have the ability, use energy minimization to get
good geometries for molecules before sending them to antechamber.

...dac

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