Re: [AMBER] **No Torsion terms

From: David A Case <>
Date: Wed, 18 Mar 2015 09:35:28 -0400

On Tue, Mar 17, 2015, Evans, Shalton wrote:

> > min_rep=loadpdb min_rep.pdb
> Loading PDB file: ./min_rep.pdb
> -- residue 1: duplicate [C138] atoms (total 2)
> -- residue 2: duplicate [C138] atoms (total 2)
> -- residue 3: duplicate [C138] atoms (total 2)
> -- residue 4: duplicate [C138] atoms (total 2)
> Warning: Atom names in each residue should be unique.
> (Same-name atoms are handled by using the first
> occurrence and by ignoring the rest.
> Frequently duplicate atom names stem from alternate
> conformations in the PDB file.)

Make sure you examine the above warnings: they may well be errors in your
> Added missing heavy atom: .R<GRA 1>.A<C135 195>

This means that your PDB file is missing an atom named "C135" in
residue 1 named GRA. This might be OK if that is what you expect, but be
aware that LEaP may build this atom in a non-optimal position.

> WARNING: There is a bond of 6.368147 angstroms between:
> ------- .R<GRA 1>.A<C138 165> and .R<GRA 1>.A<C140 168>

Obviously, you should check to see if these warnings are expected.

> ** No torsion terms for ha-c2-cc-ca

It doesn't look like you ever loaded the frcmod file that parmchk created.
You need to invoke the loadAmberParams command to do that. Also, you should
use parmchk and not parmchk2, although I don't think that is an issue here.

...good luck....dac

> Apparently I have "**No torsion terms for" multiple bonds. I looked and
> apparently I can manually input these torsion angles but I don't know
> where to find them after much time of looking. Could someone help me in
> fixing this issue.


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Received on Wed Mar 18 2015 - 07:00:02 PDT
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