normal martinize.py problem

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3 years 8 months ago #8652 by eleanorsjung
martinize.py problem was created by eleanorsjung
Hi,

I am trying to create a CG model for a peptide using martinize.py and am getting the following error.

python martinize.py -f PEPTIDE.pdb -o CGPEPTIDE.top -x CGPEPTIDE.pdb -dssp /usr/local/bin/mkdssp -p backbone -ff martini22

INFO MARTINIZE, script version 2.6
INFO If you use this script please cite:
INFO de Jong et al., J. Chem. Theory Comput., 2013, DOI:10.1021/ct300646g
INFO Chain termini will be charged
INFO Residues at chain brakes will not be charged
INFO The martini22 forcefield will be used.
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 PDB file.
INFO Found 1 chains:
INFO 1: (Protein), 207 atoms in 9 residues.
INFO Total size of the system: 9 residues.
Traceback (most recent call last):
File "martinize.py", line 4792, in <module>
main(options)
File "martinize.py", line 4480, in main
ss += chain.dss(method, executable)
File "martinize.py", line 3289, in dss
self.set_ss(ssDetermination[method](self, atomlist, executable), source=method)
File "martinize.py", line 2654, in call_dssp
for line in open(ssdfile).readlines():
IOError: [Errno 2] No such file or directory: 'chain_.ssd'

A similar problem has come up in this forum before ( http://md.chem.rug.nl/index.php/component/kunena/9-tools/4319-dssp-broken-pipe-error ), but I don't know what changes to make to the pdb file. If I need to create an ssd file, are there any ideas on how do it?

Thanks. Any help is much appreciated.

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3 years 7 months ago #8657 by peterkroon
Replied by peterkroon on topic martinize.py problem
Hey,

just run dssp on PEPTIDE.pdb. I.e. dssp -i PEPTIDE.pdb -o my_peptide.ssd.
If that doesn't work, it should at least tell you a bit more about what's wrong with your pdb file.

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