[gmx-users] cgenff charm error

LAM, Tsz Nok z.noklam at link.cuhk.edu.hk
Thu Sep 13 13:16:35 CEST 2018

Hi Marzieh,

I don't think the error is related to python version, but the naming of the files. Maybe the script needs that your input files are also named as LIG.str and LIG.mol2, something like that.

What I do know about the script when using it before, is that it requires an older version of python package "networkx" (I tested that version 1.9 worked). If you see further errors, you may want to try pip and virtualenv to use the appropriate packages, e.g.:

$ sudo apt install virtualenv pip
$ virtualenv new_directory  # making virtualenv directory with tools inside
$ source virtual/bin/activate  #activating virtualenv
$ pip install network==1.9   #specify to use version 1.9
$ pip install numpy

Then your script should work fine (You can deactivate virtualenv afterwards). More on pip and virtualenv:

Wish you luck!
LAM Tsz-Nok
School of Life Sciences, The Chinese University of Hong Kong
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of marzieh dehghan <dehghanmarzieh at gmail.com>
Sent: Thursday, September 13, 2018 6:17:09 PM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] cgenff charm error

Dear all
I used charm36 and cgenff (http://mackerell.umaryland.edu/charmm_ff.shtml)
to convert str format of ligand to itp format. when I used the following

python cgenff_charmm2gmx.py LIG lig.mol2 lig.str charmm36-jul2017.ff/

I confront this error:

NOTE1: Code tested with python 2.7.3. Your version: 2.7.12 (default, Dec  4
2017, 14:50:18)
[GCC 5.4.0 20160609]

NOTE2: Please be sure to use the same version of CGenFF in your simulations
that was used during parameter generation:
Traceback (most recent call last):
  File "cgenff_charmm2gmx.py", line 777, in <module>
    check_versions(rtp_name,ffdir + "/forcefield.doc")
  File "cgenff_charmm2gmx.py", line 53, in check_versions
    f = open(str_filename, 'r')
IOError: [Errno 2] No such file or directory: 'LIG1.str'

I installed python 2.7.3 for ubuntu, but it seems that it has not been
please let me know how to solve this error

Thanks a lot

*Marzieh DehghanPhD of BiochemistryInstitute of biochemistry and Biophysics
(IBB)University of Tehran, Tehran- Iran.*
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