Hello.
Thank you for your help.
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
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 ){
aAtomA = aAtomBondedNeighbor(saPAtom->aAtom, 0);
if( sAtomType(aAtomA)[0] == 'C' ||
sAtomType(aAtomA)[0] ==
'c' ) dGBrad = 1.3;
if( sAtomType(aAtomA)[0] ==
'O' ||
sAtomType(aAtomA)[0] ==
'o' ) dGBrad = 0.8;
if( sAtomType(aAtomA)[0] ==
'S' ||
sAtomType(aAtomA)[0] ==
's' ) dGBrad = 0.8;
if( (sAtomType(aAtomA)[0] ==
'N' ||
sAtomType(aAtomA)[0] ==
'n') &&
GDefaults.iGBparm ==
2) dGBrad = 1.3;
}
if( GDefaults.iGBparm == 6 ){ /* try
Alexey's scheme */
aAtomA =
aAtomBondedNeighbor(saPAtom->aAtom, 0);
if( sAtomType(aAtomA)[0] ==
'N' ||
sAtomType(aAtomA)[0] ==
'n' ) dGBrad = 1.3;
}
break;
case 6: dGBrad = 1.7; break;
case 7: dGBrad = 1.55; break;
case 8: dGBrad = 1.5; break;
case 9: dGBrad = 1.5; break;
case 14: dGBrad = 2.1; break;
case 15: dGBrad = 1.85; break;
case 16: dGBrad = 1.8; break;
case 17: dGBrad = 1.7; break;
default: dGBrad = 1.5; break;
############################################################################
############################
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.
Thanks in advance.
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Received on Wed Jul 23 2003 - 12:53:01 PDT
