AMBER Archive (2007)

Subject: Re: AMBER: frcmod

From: Brooke Elizabeth Adams (badams11_at_mix.wvu.edu)
Date: Mon Jun 18 2007 - 14:06:34 CDT

When using the GAFF, either not included, -at gaff, or -at GAFF, the
frcmod output file did not include all the atoms, bonds, or information
needed. It was just left blank. I am not sure why it did this, however,
the problem still lies in finding the relationship of:

CZ - P - NT or c1 - p5 - n3, still looking for force numbers

(the input file is the same, with the code,
antechamber -i tabun_2_A02.pdb -fi pdb -o TAB.prepi -fo prepi -at GAFF
-rn TAB -c bcc&
(also -at gaff and nothing)

----- Original Message -----
From: "David A. Case" <case_at_scripps.edu>
Date: Friday, June 15, 2007 5:47 pm
Subject: Re: AMBER: frcmod
To: amber_at_scripps.edu
Cc: jwang_at_encysive.com

> On Fri, Jun 15, 2007, Brooke Elizabeth Adams wrote:
>
> > Here are the files,
> > and the command for antechamber
> >
> > antechamber -i tabun_2_A02.pdb -fi pdb -o TAB.prepi -fo prepi -at
> AMBER
> ^^^^^^^^^
>
> Remove this flag. Generally, the gaff forcefield is *much* more
> completethan is the attempt to use AMBER atom types for strange
> environments. The
> only time -at AMBER should be used (in my view, Junmei may want to
> weigh in
> here) is if you have a minor modification of an amino acid or
> nucleotide, and
> want to see if the modified residue can be reasonably accommated
> with the
> existing Amber types.
>
> I ran your files using gaff types, and there were no missing
> parameters. If
> you *really* need Amber types, you might still run with GAFF, and
> use the GAFF
> values as a first guess for what the corresponding Amber types
> would be. But
> I am not recommending this, just pointing is out as a possibility.
>
> ...hope this helps...dac
>
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