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',
'pdb4amber')()
File
"/home/crlc-xeon/amber18/lib/python2.7/site-packages/pdb4amber-1.6.dev0-py2.7.egg/pdb4amber/pdb4amber.py",
line 818, in main
arg_noter=opt.noter)
File
"/home/crlc-xeon/amber18/lib/python2.7/site-packages/pdb4amber-1.6.dev0-py2.7.egg/pdb4amber/pdb4amber.py",
line 505, in run
parm = parmed.load_file(pdbin)
File
"/home/crlc-xeon/amber18/lib/python2.7/site-packages/ParmEd-3.0.0+57.g74a84d30-py2.7-linux-x86_64.egg/parmed/formats/registry.py",
line 197, in load_file
return cls.parse(filename, *args, **kwargs)
File
"/home/crlc-xeon/amber18/lib/python2.7/site-packages/ParmEd-3.0.0+57.g74a84d30-py2.7-linux-x86_64.egg/parmed/formats/pqr.py",
line 133, in parse
if words[0] in ('ATOM', 'HETATM'):
IndexError: list index out of range
Regards,
--
D L Senal Dinuka
Grad.Chem., A.I.Chem.C.
Research Assistant
College of Chemical Sciences
Institute of Chemistry Ceylon
Rajagiriya
Sri Lanka
+94 77 627 4678
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Received on Thu May 24 2018 - 03:30:02 PDT
