[gmx-users] chiara_marcolin wants to share a link | Gromacs

rossen at kth.se rossen at kth.se
Wed Feb 4 11:49:44 CET 2015

chiara_marcolin wants to a share a link on the Gromacs wiki: http://www.gromacs.org/

chiara_marcolin says:
 I am trying to run Protein Martini tutorial using Ubuntu 14.04 and Gromacs software.

When I run this command: "python martinize.py -f 1UBQ.pdb -o system.top -x 1UBQ-CG.pdb -dssp /usr/bin/do_dssp -ff martini22"

 I get this error message:

Traceback (most recent call last):
  File "martinize.py", line 5064, in <module>
  File "martinize.py", line 4744, in main
    ss += chain.dss(method, executable)
  File "martinize.py", line 3636, in dss
  File "martinize.py", line 882, in call_dssp
    if atom[0][0]!='H' and atom[0][:2]!='O2': p.stdin.write(pdbOut(atom))
IOError: [Errno 32] Broken pipe

 and I do not know how to fix it.

Could anyone help me please?
Thanks in advance
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