AMBER Archive (2008)

Subject: Re: AMBER: mbondi radii for gaff atom types

From: David A. Case (case_at_scripps.edu)
Date: Wed May 28 2008 - 12:31:30 CDT

On Wed, May 28, 2008, Sara J wrote:

> I am trying to run a PB(and GB) calculation on a small molecule with GAFF
> atom types. In my tleap script, I have added the following lines to generate
> the prmtop file with GAFF atom types and to use modified Bondi radii:
>
> I am bit worried to see the radii for ho and hc atom type. When I look through the code of leap (/src/leap/src/leap/unitio.c ;
> line 5212), I see the following:
> if( GDefaults.iGBparm == 1 || GDefaults.iGBparm == 2 ) {
> 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;

> (note that I have changed the atom types to lower case to be compatible with
> gaff type)

I don't see why you modified the codes, as the revision doesn't (seem to?)
make much sense.

> According to this code, the 'h' bonded to 'c' should have 1.3 and bonded to
> 'o' should have 0.8 radii, but I dont see that in my prmtop. I would really
> appreciate if someone can point me in the right direction. Am I generating
> the right prmtop file? If yes, why aren't the radii correct?

Are you sure you are going through this code path (i.e. that GDefaults.iGBparm
has the value you think it has?) I'd recommend double-checking by printing
out some debug messages. (You didn't report what LEaP commands you acutally
used....)

...dac

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