It might be worthwhile to consider the energy column in the pdf: At RT we have about 0.6 kcal/mol thermal energy, so a *single attractive* vdW interaction has little impact - it is generally the sum of many of those contributing to notable and important attractive forces. For a *single repulsive* (steep branch) vdW this is quite different - your quickly get energetically significant repulsions even for one bad contact. So the vdW repulsion are both useful (nearly independent) stereochemical restraints and a good indicator for improbable conformations (see molprobity clash score, rama, etc).
BR -----Original Message----- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Nadir T. Mrabet Sent: Wednesday, July 15, 2009 7:10 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Van der Waals contacts This issue is far from being trivial. To address the question, I recommend looking at this simple example (attached pdf file) which shows that even when the atom distance is twice the vdw diameter, there is still attraction between atoms (unified type, with implicit H atoms). Some, but not all, consider that water screens out interactions, that is, the vdw interaction is attractive provided that R < Rm + 2 x R(H2O). But then, one may also need to consider the special case of water-mediated H-bonds, where the heavy atoms being considered are polar. HTH, Nadir Pr. Nadir T. Mrabet Cellular & Molecular Biochemistry INSERM U-954 Nancy University, School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy Cedex France Phone: +33 (0)3.83.68.32.73 Fax: +33 (0)3.83.68.32.79 E-mail: nadir.mra...@medecine.uhp-nancy.fr Cell.: +33 (0)6.11.35.69.09 LEGAL NOTICE Unless expressly stated otherwise, this message is confidential and may be privileged. It is intended for the addressee(s) only. Access to this E-mail by anyone else is unauthorized. If you are not an addressee, any disclosure or copying of the contents of this E-mail, or any action taken (or not taken) in reliance on it, is unauthorized and may be unlawful. If you are not an addressee, please inform the sender immediately. Clayton, Gina Martyn wrote: > > Hi CCP4ers > > Perhaps I am hashing over old news...but > > We are having a discussion about Van Der Waals contacts and effective > contacts i.e. the "real distance" of a VDW bump between say a CH and a > CH group which sometimes is described as between a C and a C as i.e. > 2x 1.6A and ending about 4A but not including hydrogen. > > Some programs list contacts, to say a ligand, as far as 6A apart and > some of the simulation programs use that distance too for contacts for > protein protein interactions. > > Does anyone know of a good paper that discusses the effective distance > or has a comment on where a VDW force may begin and end or it's > effective distance - though some say it never truly ends just > approaches zero... > > > G > > > > Notice: This e-mail message, together with any attachments, contains > information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, > New Jersey, USA 08889), and/or its affiliates (which may be known > outside the United States as Merck Frosst, Merck Sharp & Dohme or MSD > and in Japan, as Banyu - direct contact information for affiliates is > available at http://www.merck.com/contact/contacts.html) that may be > confidential, proprietary copyrighted and/or legally privileged. It is > intended solely for the use of the individual or entity named on this > message. If you are not the intended recipient, and have received this > message in error, please notify us immediately by reply e-mail and > then delete it from your system. >
