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 : 2b8 NOTE3: In order to avoid duplicated parameters, do NOT select the 'Include parameters that are already in CGenFF' option when uploading a molecule into CGenFF. 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, Yana -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.