[gmx-users] cgenff charm error

Justin Lemkul jalemkul at vt.edu
Thu Sep 13 13:26:14 CEST 2018

On 9/13/18 6:17 AM, marzieh dehghan wrote:
> Hi
> 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
> command:
> 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'

The error is quite simple: LIG1.str does not exist in the working 
directory. This also means that what you posted above for your command 
is not at all what you actually typed. Please always copy and paste 
commands from your terminal rather than trying to re-create what you did.

> I installed python 2.7.3 for ubuntu, but it seems that it has not been
> installed.

You don't need Python 2.7.3; the script is merely advising you of what 
has been used for testing in the event that there is an actual 
Python-related issue.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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