On 7/9/14, 10:11 AM, Nikolaos Michelarakis wrote:
Hey, Thanks a lot, I fixed the file but I am now getting a python error, I think. Traceback (most recent call last): File "./cgenff_charmm2gmx.py", line 792, in <module> m.read_mol2_coor_only(mol2_name) File "./cgenff_charmm2gmx.py", line 720, in read_mol2_coor_only atomi = int(entry[0])-1 ValueError: invalid literal for int() with base 10: '' something wrong with the coordinates? the new mol2 file is: https://drive.google.com/file/d/0BzqRbRx4Ynf0SV9rZnhhTmxGRmM/edit?usp=sharing
I'll have to dig into this a bit more closely, but it's not something I have time for at the moment. Adding some print statements to the Python script will tell you exactly what's going on.
Also note that your mol2 file will still generate problems because all of your H atoms are named simply "H" rather than the actual name assigned in the .str file, so you're going to have problems there, as well. The script is intended to parse the matching output from a mol2 file submitted to ParamChem, so any other use of the script will require some occasional hacking, workarounds, or caveats for input files.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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.