In message <[EMAIL PROTECTED]> (on 7 June 2008 22:50:24 +0200), [EMAIL PROTECTED] (David van der Spoel) wrote:
>No, this does mean that it comes from vdwradii.dat. If there are missing >atoms you can just add them to the file. The only issue is that there >are different sets of radii in use. Which one to use depends on the >application. A patch to change vdwradii.dat to radii preferable for genbox and other bump-checking uses can be found under http://cesario.rutgers.edu/easmith/research/patches/. They are largely taken from reduce (by the Richardsons)'s explRad. It doesn't include phosphorus, since I was working purely with proteins when I created it, but it should not be difficult to add it; below is a copy of the relevant section from reduce's sourcecode (in ElementInfo.C, version 3.03.061020). -Allen // For non-metals, explicit VDW radii from // Gavezzotti, J. Am. Chem. Soc. (1983) 105, 5220-5225. // or, if unavailable, // Bondi, J. Phys. Chem. (1964), V68, N3, 441-451. // Covalent and ionic radii from // Advanced Inorganic Chemistry, Cotton & Wilkinson, 1962, p93. // atno explRad implRad covRad mageColors flags insert( 0, "?", "unknown", 1.00, 0.00, 0.00, "magenta", 0); insert( 0, "ignore", "ignore", 0.00, 0.00, 0.00, "magenta", IGNORE); insert( 1, "H", "hydrogen", 1.17, 0.00, 0.30, "grey", 0); insert( 1, "Har","hydrogen(aromatic)", 1.00, 0.00, 0.30, "grey", 0); insert( 1, "Hpol","hydrogen(polar)", 1.00, 0.00, 0.30, "grey", DONOR_ATOM); insert( 1, "Ha+p", "hydrogen(aromatic&polar)", 1.00, 0.00, 0.30, "grey", DONOR_ATOM); insert( 1, "HOd", "hydrogen(omnidirectional)", 1.00, 0.00, 0.30, "grey", DONOR_ATOM|HB_ONLY_DUMMY); insert( 6, "C", "carbon", 1.75, 1.90, 0.77, "white", 0); insert( 6, "Car","carbon(aromatic)", 1.75, 1.90, 0.77, "white", ACCEPTOR_ATOM); insert( 6, "C=O","carbon(carbonyl)", 1.65, 1.80, 0.77, "white", 0); //** seems to help insert( 7, "N", "nitrogen", 1.55, 1.70, 0.70, "sky", 0); insert( 7, "Nacc","nitrogen(acceptor)",1.55, 1.70, 0.70, "sky", ACCEPTOR_ATOM); insert( 8, "O", "oxygen", 1.40, 1.50, 0.66, "red", ACCEPTOR_ATOM); insert(15, "P", "phosphorus", 1.80, 1.80, 1.10, "pink", 0); insert(16, "S", "sulfur", 1.80, 1.90, 1.04, "yellow", ACCEPTOR_ATOM); insert(33, "As", "arsnic", 2.00, 2.10, 1.21, "grey", 0); insert(34, "Se", "selenium", 1.90, 2.00, 1.17, "green", 0); insert( 9, "F", "fluorine", 1.30, 1.30, 0.58, "green", ACCEPTOR_ATOM); insert(17, "Cl", "chlorine", 1.77, 1.77, 0.99, "green", ACCEPTOR_ATOM); insert(35, "Br", "bromine", 1.95, 1.95, 1.14, "brown", ACCEPTOR_ATOM); insert(53, "I", "iodine", 2.10, 2.10, 1.33, "brown", ACCEPTOR_ATOM); -- Allen Smith, Ph.D. http://cesario.rutgers.edu/easmith/ September 11, 2001 A Day That Shall Live In Infamy II "They that can give up essential liberty to obtain a little temporary safety deserve neither liberty nor safety." - Benjamin Franklin _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
