AMBER Archive (2003)

Subject: Re: AMBER: FILE UNITIO.C

From: David A. Case (case_at_scripps.edu)
Date: Wed Jul 23 2003 - 10:04:54 CDT

On Wed, Jul 23, 2003, Obdulia Rabal wrote:
>
> The reference I mean is J.Phys.Chem.B.2001,105,11314-11325 and bondi radii I
> saw are in table 7, which are:
>
> H(C)=1.30
> H(N)=1.20
> H(O)=0.80
> C=1.70
> O=1.50
> N=1.55
> P=1.85

These are the "mbondi" (modified Bondi) radii, *not* the bondi radii.
It seems to me that the user manual is pretty clear about this, but we'll
try to put an actual table in for the next release.

>
> As I understand, the following lines refer to these radii in file unitio.c:
>
> ############################################################################
> if( GDefaults.iGBparm < 3 || GDefaults.iGBparm == 6 ) {
> /* Bondi or modified Bondi radii */
> switch( iElement ){
> case 1: dGBrad = 1.2;
>
> /* make the modifications that hydrogen radii
> depend upon the atom it is bonded to. iGBparm=1
> corresponds to Amber 6, and JACS 122:2489 (2000);
> iGBparm=2 adds the modifcation from Biopolymers
> 56: 275 (2001) */
>
> if( GDefaults.iGBparm == 1 || GDefaults.iGBparm == 2 ){

                          [H-atom assignment code here]

> }
>
>
> ############################################################################
>
> So I thought when typing "set default PBradii bondi" in xleap and saving
> prmtop file, %FLAG_RADII should be the same as they appear in these lines.

When you set default PBradii bondi, the iGBparm variable is set to zero, hence
the above code snippet shows that all hydrogens will have the same radius
(1.2). This is consistent with what the manual says.

..dac 

-- 

==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
==================================================================
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu