Hi Rafael, It's normal for the vdW analysis to be different when using different methods (e.g., due to different atomic radius definitions). However, the reporting of a very bad clashscore by MolProbity requires a closer look.
Over the past few years, we've revised Xplor-NIH's nonbonded parameters to make them more compatible with MolProbity, including the creation of a new repulsive energy term. The latter is described in a 2018 publication (Bermejo & Schwieters, Methods Mol. Biol. 2018, 1688, 311-340), and included in the examples within the installation directory (e.g., eginput/gb1_rdc/fold.py). Please, make sure you are using an updated version of Xplor-NIH and the above-mentioned nonbonded term. Let me know if you have further questions. Best, Guillermo ------------------------ Hello, I performed a simulation with the program and obtained the structures without any VdW violation according to the output file. Then I tried to validate my structures using wwpdb and the program recognized a lot of clashes. Is this an error in the force field? Should I perform any other calculations? Is it normal this kind of clashes? Thanks in advance for your help, Rafael RodrÃguez ________________________________ To unsubscribe from the XPLOR-NIH list, click the following link: http://list.nih.gov/cgi-bin/wa.exe?SUBED1=XPLOR-NIH&A=1 CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe. ######################################################################## To unsubscribe from the XPLOR-NIH list, click the following link: http://list.nih.gov/cgi-bin/wa.exe?SUBED1=XPLOR-NIH&A=1
