Re: [AMBER] question about gaps

From: Gordon Richard Chalmers <>
Date: Sun, 29 Nov 2020 18:41:30 +0000

Thank you.

I will rewrite the software to make sure the order of residues are
correct. TLeap manages the linear backbone peptide sequence
input correctly. The C-N bond should be usually 1.32 A, and it is.

I am working a new GA with the Amber force field that finds local energy
conformational minima by changing dihedral angles. It takes in a sequence
and the amino acid templates, but there could be an issue with going from
N to C terminals instead of C to N.

From: David A Case <>
Sent: Sunday, November 29, 2020 1:26 PM
To: AMBER Mailing List <>
Subject: Re: [AMBER] question about gaps


On Sun, Nov 29, 2020, Gordon Richard Chalmers wrote:
>I have a question about gaps that I will be solving
>soon. Why does my Matlab protein structure software
>produce this when using pdb4amber:

>---------- Gaps (Renumbered Residues!)
>gap of 3.180778 A between MET 1 and PRO 2
>gap of 3.532217 A between PRO 2 and LEU 3

First, what value you do get when you compute the distance between the C
of residue 1 and the N of residue 2?

>Attaching the pdb files exceeds the Amber reflector memory limit.

Since you get the message above between residues 1 and 2, it seems you
could post a small portion of the pdb file. Finding a small example
that illustrates problems is generally a good idea anyway.


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