I am trying to generate my input file for CHARMM force field using CGenff website.
after using the python script :
python cgenff_charmm2gmx_py2.py lig lig.str charmm36.ff
I got the error:
Usage: RESNAME lig.mol2 lig.str charmm36.ff
this happens while my .str and .mol2 file has the exact name mentioned in the python file (i.e lig)
I would be grateful if anyone helps me.
You aren’t providing a .mol2 file name in your command.
oh! you are right. how about this one? should I change the script version? my python version is 2.7
How did you generate the
lig.str file? If it came from a source other than ParamChem/CGenFF, it will not be compatible with our conversion utility.
I used CGennFF website.
seems the problem arises from the version of CGennFF used in ff and by website. right?
I have no idea how the script could have given you that error. It looks for the “For use with CGenFF version” string and checks for a match against the force field. Here, both are 4.4 so there should be no issue.
should I use other servers?
Have you edited the stream file in any way, or opened it in a non-plain text editor that would cause problems with line endings?
If you can upload your
.str files, I will look into this.
Unfortunately these formats are not allowed to be uploaded here. Moreover, I can not upload more than one file since I am new to this website.
Upload to Google Drive and post the link. Please make sure permissions are set correctly so that the files can be accessed by anyone with the link (not via email address).
I can’t reproduce the error. The conversion works perfectly for me.
is there probably something wrong in my python script?
Looking back at your screenshot, your command is still wrong. Residue name, then mol2, then stream file. You inverted the stream and mol2 files.
awsome! you are right ! it worked. thanks a milion!