Re: [AMBER] Peptide with non-standard residues

From: David Case <>
Date: Fri, 27 Jan 2017 09:39:27 -0500

On Fri, Jan 27, 2017, Andreas Tosstorff wrote:
> I am trying to generate a peptide with three non standard residues: pGlu
> (aka PCA) - His - Gly
> I tried generating tha parameter files for PCA in antechamber and then
> load it into leap.
> I cannot save the parameter files of the resulting peptide, because
> several bond, angle and torsion parameters are missing.

*Which* parameters are missing? (Aside: my usual complaint: users seem
very wary of posting exact error messages, but the details are often most

Did you run parmchk2, which will look for any missing parameters, and generate
gueses? (This is relevant if the missing parameters involve only gaff atom

Or, are the missing parameters between Amber atom types (upper-case atom
types) and gaff (lower-case atom types)? You may have to find the analogous
Amber types and enter them by hand into a frcmod file. An alternative, which
I would recommend for a modified amino acid where the modification is well
out on the side chain: ask antechamber to use Amber atom types. You may still
need to manually copy gaff parameters to the corresponding Amber atom types,
but the backbone behavior will then follow that of the Amber force field you
are using.

...good luck...dac

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Received on Fri Jan 27 2017 - 07:00:02 PST
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