[AMBER] Error in using pdb4amber command

From: senal dinuka <senal.ichemc.edu.lk>
Date: Thu, 24 May 2018 15:44:03 +0530

Dear Amber Users,
I am using Amber 16 along with Amber Tools 18 version. I was able to
successfully perform pdb4amber command on original crystal structure
(1GQR). But after protonation via H++ server and resubmitting for pdb4amber
following error occurs.
I really appreciate an insight on this.

Summary of pdb4amber for: 80_20_pH.pdb
Traceback (most recent call last):
  File "/home/crlc-xeon/amber18/bin/pdb4amber", line 11, in <module>
    load_entry_point('pdb4amber==1.6.dev0', 'console_scripts',
line 818, in main
line 505, in run
    parm = parmed.load_file(pdbin)
line 197, in load_file
    return cls.parse(filename, *args, **kwargs)
line 133, in parse
    if words[0] in ('ATOM', 'HETATM'):
IndexError: list index out of range

D L Senal Dinuka
Grad.Chem., A.I.Chem.C.
Research Assistant
College of Chemical Sciences
Institute of Chemistry Ceylon
Sri Lanka
+94 77 627 4678
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Received on Thu May 24 2018 - 03:30:02 PDT
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