Re: [AMBER] IndexError in pdb4amber

From: He, Amy via AMBER <amber.ambermd.org>
Date: Thu, 4 Jul 2024 00:16:45 +0000

Hi Noureen,

This might be caused by two partially missing residues, PRO A 93 and LYS B 2:

REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 PRO A 93 N CA CB CG CD
REMARK 470 LYS B 2 N CB CG CD CE NZ

A dirty walkaround to make pdb4amber work is to remove the two residues from your file. But depending on what you want to use the structure for, you might want to repair the missing atoms and residues.

Hope this is mildly helpful! 


--
Amy He
Forli Lab @ TSRI
yihe.scripps.edu
From: Abdelrahman, Noureen via AMBER <amber.ambermd.org>
Date: Wednesday, July 3, 2024 at 6:44 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] IndexError in pdb4amber
Hello,
I am trying to run pdb4amber on the attached pdb file to clean it up for tleap, but I am getting this error: IndexError: list index out of range .
I tried renumbering the residues, but that didn't work. I suspect that is caused by the missing residues, but I am not entirely sure. Any help would be appreciated!
Thanks,
Noureen
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Received on Wed Jul 03 2024 - 17:30:02 PDT
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