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 <david.case.rutgers.edu>
Sent: Sunday, November 29, 2020 1:26 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] question about gaps
[EXTERNAL SENDER - PROCEED CAUTIOUSLY]
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.
....dac
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Received on Sun Nov 29 2020 - 11:00:03 PST
