[gmx-users] problems with martinize.py
tsjerkw at gmail.com
Mon Feb 20 13:27:19 CET 2012
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]), " ",
> ValueError: invalid literal for int() with base 10: '2.'
> Can anyone help me on that?
> gmx-users mailing list gmx-users at gromacs.org
> 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.
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
More information about the gromacs.org_gmx-users