[gmx-users] Vdwradii.dat uses (was Re: g_sas Vdwradii.dat)

[Allen Smith]

In message <484AF490.10708 at xray.bmc.uu.se> (on 7 June 2008 22:50:24 +0200),
spoel at xray.bmc.uu.se (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