[gmx-users] (no subject)
fhyt at chem.uni-sofia.bg
Mon Jul 14 12:17:47 CEST 2014
Firstly, I want to thank Justin Lemkul for helping me on the topic
"polarizable water and non-polarizable alkanes". Now I have to
simulate systems that consist of polarizable water and polarizable alkanes.
The chosen force field is CHARMM with Drude oscillators.
I am trying to use the python script cgenff_charmm2gmx.py to generate the
needed files, but the following error occurs:
NOTE1: Code tested with python 2.7.3. Your version: 2.6.6 (r266:84292, Jan
22 2014, 09:42:36)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]
NOTE2: Please be sure to use the same version of CGenFF in your simulations
that was used during parameter generation:
--Version of CGenFF detected in charmm36-mar2014.ff//forcefield.doc :
NOTE3: In order to avoid duplicated parameters, do NOT select the 'Include
parameters that are already in CGenFF' option when uploading a molecule into
error in atomgroup.py: read_mol2_coor_only: natoms in mol2 .ne. top
I found that another person had this problem, but I still could not fix it.
I have attached the files I am using. The command line I enter is:
./cgenff_charmm2gmx.py PENT pentane.mol2
I will really appreciate if someone could help me,
Thanks in advance,
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