[gmx-users] problems with martinize.py

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Feb 20 13:27:19 CET 2012

Hi Francesca,

Is this the latest version
If it is, please send me the input file and I'll fix the bug. Note
that the previous version that was available online was one used in a
workshop, while the script was still in beta.



On Mon, Feb 20, 2012 at 10:43 AM, francesca vitalini
<francesca.vitalini11 at gmail.com> wrote:
> 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]), " ",
> 10*F(a[20:28]),10*F(a[28:36]),10*F(a[36:44]))
> ValueError: invalid literal for int() with base 10: '2.'
>  Can anyone help me on that?
> Thanks
> --
> Francesca
> --
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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