[gmx-users] problems with martinize.py

francesca vitalini francesca.vitalini11 at gmail.com
Mon Feb 20 10:43:19 CET 2012

Hi all,
I'm trying to coarsegrain my structure using the script martinize.py
and using my gro file as inmput and the dssp file with the second
structure downloaded from http://swift.cmbi.ru.nl/gv/dssp using the
pdb structure as input, I get the following error message that I
really don't understand.

INFO       Chain termini will be charged
INFO       Residues at chain brakes will not be charged
INFO       Local elastic bonds will be used for extended regions.
INFO       Position restraints will be generated.
WARNING    Position restraints are only enabled if -DPOSRES is set in
the MDP file
INFO       Read input structure from file.
INFO       Input structure is a GRO file. Chains will be labeled consecutively.
Traceback (most recent call last):
  File "./martinize.py", line 2037, in <module>
    for title,atoms,box in frameIterator(inStream):
  File "./martinize.py", line 1303, in groFrameIterator
    atoms  = [groAtom(streamIterator.next())  for i in range(natoms)]
  File "./martinize.py", line 1290, in groAtom
    return (S(a[10:15]), S(a[5:10]),   I(a[:5]), " ",
ValueError: invalid literal for int() with base 10: '2.'

 Can anyone help me on that?


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