Hi Charles, Thanks for the clarification. I'm not using a different version of XPLOR-NIH, but I am using parameter and topology files that have been extensively modified by us.
Thanks again, Keith Keith L. Constantine, Ph. D. Sr. Research Investigator II Mechanistic Biochemistry Bristol Myers Squibb Research and Development P.O. Box 4000 Princeton, NJ 08543-4000 Tel: (609)-252-6926 Fax: (609)-252-6012 e-mail: keith.constant...@bms.com >-----Original Message----- >From: Charles Schwieters [mailto:char...@schwieters.org] >Sent: Monday, October 21, 2013 3:44 PM >To: Constantine, Keith >Cc: Charles Schwieters; xplor-...@nmr.cit.nih.gov; Mueller, Luciano; >Metzler, William >Subject: Re: changing van der Waals radius without modifying an atom >type > > >Hi Keith-- > >> >> I'm using a somewhat older force field (see below. The Lennard-Jones >> potential is implemented differently. > >Are you using a different version of Xplor-NIH than what we distribute? > >> For example S (radius = 1.05 angstroms) > >That seems rather short. > >> sigma is 3.7458 in this setup. After double checking the >> formula given (sigma*2^(-5/6))I believe is wrong - it should include >> division by 2 . So for S I get 3.7458(0.561)/2 = 1.05 angstroms. >> >> I pretty sure the sigma I should use is 4.635 to approximate r = 1.20 >> angstroms. >> > >In the nonbonded VDW potential used in Xplor-NIH, > > http://nmr.cit.nih.gov/xplor-nih/doc/2.34/xplor/node118.html >(hopefully this is working by the time you look) > >the basic form of the potential is: > > E = sigma^12/R^12 - sigma^6 /R^6 > >where R is the interatomic distance, not radius (rather, it's 2*radius >for interactions between two of the same type of atoms). > >The minimum in this energy is at > > R = sigma * 2^(1/6). > >Therefore, atomic radius = sigma * 2^(1/6) / 2 = sigma * 2^(-5/6) > >best regards-- >Charles This message (including any attachments) may contain confidential, proprietary, privileged and/or private information. The information is intended to be for the use of the individual or entity designated above. If you are not the intended recipient of this message, please notify the sender immediately, and delete the message and any attachments. Any disclosure, reproduction, distribution or other use of this message or any attachments by an individual or entity other than the intended recipient is prohibited. _______________________________________________ Xplor-nih mailing list Xplor-nih@cake.cit.nih.gov http://cake.cit.nih.gov/mailman/listinfo/xplor-nih
