[gmx-users] problems with martinize.py

[Tsjerk Wassenaar]

Hi Francesca,

Is this the latest version
(http://md.chem.rug.nl/cgmartini/index.php/downloads/tools/204-martinize)?
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.

Cheers,

Tsjerk


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
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists



-- 
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