Hello I am receiving the error:
'utf-8' codec can't decode byte 0xa9 in position 11: invalid start byte
when I visualize my HETATM PDB File via Pymol that I extracted from my docked protein-complex, please let me know how to amend this if known, see attachment.
Thanks if you can assist:)
How do you extract your file? And why you called it HETATAM PDB?
The files PK "6©#V^Æ2 ' ' mimetypeapplication/vnd.oasis.opendocument.textPK 6©#V meta.xmlSMs›0¼÷Wxh¯ OcÐ`rë©™t&îLnYzÆ´Xb„ Ò_± :p@ûvÙ·ORñð~hoàºÚšuD -À(«kS£_›ïq=”_
»ÛÕ...........
It looks like there is a syntax error.
Hello Sahadot thank you so much for your kind update:).
I had a protein-ligand complexed generated via Medusadock, now I am performing a simulation of this complex via Gromacs. Accordingly for this Gromacs Tutorial I would need to first separate the protein from the ligand to generate the topologies, I cut and pasted the ligand portion out which is what I attached. Were you able to successfully view the 14C.pdb file that I attached to my original inquiry? I do not know nor understand what you had written that begins with `The files PK...´ and I only titled this HETATM PDB since it exhibits HETATMs and is in a pdb format.
Hopefully this makes sense, please let me know what you think, thanks Sahadot:).
Hi Sahadot and others you can disregard my last inquiry since I just generated the proper .mol2 file via Pymol i.e. I just removed all the chains leaving the ligand (thanks Maysaa;), see attached for enrichment.
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