Re: [AMBER] question about gaps

From: David A Case <>
Date: Sun, 29 Nov 2020 13:26:03 -0500

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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Received on Sun Nov 29 2020 - 10:30:03 PST
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