[gmx-users] CHARMM to GROMACS conversion and inclusion of bonded, non-standard residues and parameters

Justin Lemkul jalemkul at vt.edu
Wed Jul 9 19:30:12 CEST 2014

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 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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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