That is 1.30 angstroms. Thanks again. 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: Constantine, Keith >Sent: Monday, October 21, 2013 8:36 AM >To: 'Charles Schwieters' >Cc: xplor-...@nmr.cit.nih.gov; Mueller, Luciano; Metzler, William >Subject: RE: changing van der Waals radius without modifying an atom >type > > >Hi Charles, > > >Thanks! > >I'm using a somewhat older force field (see below. The Lennard-Jones >potential is implemented differently. For example S (radius = 1.05 >angstroms) 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. > > > Keith > >! the non-bonded parameters are approximately the same as >! DISMAN's large radii for repel=0.9, and as DISMAN's small >! radii for repel=0.75. (ECEPP2) >! the epsilon values are generally not used (and should not be) >! with this force field >! the radius is sigma*2^(-5/6) >! >! eps sigma eps(1:4) sigma(1:4) repel: 1.0 >0.9 0.8 0.75 >! >radii > nonbonded C 0.0903 3.3409 0.0903 3.3409 ! >1.875 1.688 1.5 1.406 > NONBonded C6R 0.05000 3.6349 0.10000 3.1360 ! added >02/19/10 kc from quanta params > NONBonded CA 0.120 3.3409 0.120 3.3409 > NONBonded CB 0.145 3.3409 0.145 3.3409 > NONBonded CC 0.145 3.3409 0.145 3.3409 > NONBonded CN 0.145 3.3409 0.145 3.3409 > NONBonded CP 0.1450 3.3409 0.1450 3.3409 > NONBonded CR 0.1200 3.3409 0.1200 3.3409 > nonbonded CT 0.0903 3.3409 0.0903 3.3409 > NONBonded CV 0.1200 3.3409 0.1200 3.3409 > NONBonded CW 0.1200 3.3409 0.1200 3.3409 > NONBonded CX 0.1450 3.3409 0.1450 3.3409 > nonbonded H 0.0498 2.2272 0.0498 2.2272 ! >1.250 1.125 1.0 0.9375 > nonbonded HRNE 0.0498 2.2272 0.0498 2.2272 ! >1.250 1.125 1.0 0.9375 > nonbonded HA 0.0045 2.2272 0.0045 2.2272 > nonbonded HC 0.0498 2.2272 0.0498 2.2272 > nonbonded N 0.1592 3.0068 0.1592 3.0068 ! >1.688 1.519 1.350 1.266 > NONBonded NA 0.1592 3.0068 0.1592 3.0068 > NONBonded NB 0.1592 3.0068 0.1592 3.0068 > nonbonded NC2 0.1592 3.0068 0.1592 3.0068 > nonbonded NH1 0.1592 3.0068 0.1592 3.0068 > nonbonded NH2 0.1592 3.0068 0.1592 3.0068 > nonbonded NH3 0.1592 3.0068 0.1592 3.0068 > nonbonded O 0.2342 2.7755 0.2342 2.7755 ! >1.558 1.402 1.246 1.168 > nonbonded OC 1.0244 2.7755 1.0244 2.7755 > nonbonded OH 0.2342 2.7755 0.2342 2.7755 > nonbonded S 0.0239 3.7458 0.0239 3.7458 ! >2.102 1.892 1.682 1.577 > >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: Friday, October 18, 2013 2:04 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 used: >>> >>> parameter >>> nonbond (resid X and name HN) 0.0498 4.0000 0.0498 4.000 >>> end >>> >>> If I am correct, setting sigma to 4.000 should correspond to a >>> radius of ~1.30 angstroms, which is close enough for this >>> application. >>> >> >> >>Rvdw = sigma 2^(1/6) / 2 >> >>so, to get a radius of 1.3 angstrom, use sigma=2.316 angstrom. >> >>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
