On 14/10/2020 13:38, Abhilasha Thakur wrote:
I have a query related to PyRx Virtual Screening Software, Some of my ligands files are not read by PyRx. I downloaded the SDF format and then SDF to PDB conversion by Open Bable, then uploaded the ligand library into the PyRx and then set as ligands by selecting individually but some ligand shows error. I tried so hard to identify but did not get any solution so please suggest what I can do in that case. One picture of PyRx shows error in ligand, I have attached below. Please suggest what is the possible solution to solve the PyRx related issue.
Not much to go on, but the first thing that I'd check is that the ligand representation correctly describes the hybridization, protonation and explicit formal charge. That tertiary amine in the diazapine look suspicious.
HTH, Paul. ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
