AMBER Archive (2003)

Subject: RE: AMBER: FILE UNITIO.C

From: Obdulia Rabal (mrabal_at_iqs.es)
Date: Wed Jul 23 2003 - 02:51:22 CDT

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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