[gmx-users] (no subject)

Yana Tsoneva fhyt at chem.uni-sofia.bg
Mon Jul 14 12:17:47 CEST 2014

Dear colleagues,


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

17 0


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 
./drude_toppar_oct13/toppar_drude_model_2013a.str charmm36-mar2014.ff


I will really appreciate if someone could help me,

Thanks in advance,

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