Re: [AMBER] Error in generating the residue topology for non-standard amino acid residues

From: David Case <>
Date: Thu, 28 Feb 2019 23:40:58 +0000

On Wed, Feb 27, 2019, RITUPARNA ROY wrote:

>loadamberprep pro4.prepi
>loadamberparams pro4.frcmod

Where did these files come from? And, are the atom types in it
upper or lower case? The pro4.prepi file on the tutorial web site has
all upper-case atom types. Are you sure you didn't run some other
antechamber program than those listed in the tutorial? (GAFF atom types
are lower case, whereas Amber atom types are upper case.)

>aa =sequence {ALA PR4 ALA}
>Error: Could not find bond parameter for: C - n

It looks like you parameterized PR4 using GAFF atom types, whereas ALA
from a standard library would have Amber atom types. This will not
created the cross-terms needed to put both residues in the same

A more recent tutorial on building a non-standard residue is here:

Note the use of the "-at amber" flag on antechamber runs.

...hope this helps...dac

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Received on Thu Feb 28 2019 - 16:00:02 PST
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