AMBER Archive (2007)

Subject: AMBER: Re: ff02 and ff03 parameters

From: Pavan G (pavanamber_at_gmail.com)
Date: Mon Jun 25 2007 - 14:34:30 CDT

Hello all,

>
> Recently I used amber8's ff02 and amber9's ff03 forcefields to generate
> parameters for a protein I am working on and I ended up with two different
> prmtop files. I would expect the output to be the same but here are the
> differences
>
> ff02 ff03
> 1960 1960 NATOM : total number of atoms
> 14 14 NTYPES : total number of distinct atom types
> 959 959 NBONH : number of bonds containing hydrogen
> 1025 1025 MBONA : number of bonds not containing hydrogen
> 2158 2158 NTHETH : number of angles containing hydrogen
> 1389 1389 MTHETA : number of angles not containing hydrogen
> 4149 4245 NPHIH : number of dihedrals containing
> hydrogen <-------------------- different
> 2555 2928 MPHIA : number of dihedrals not containing
> hydrogen <-------------------- different
> 0 0 NHPARM : currently not used
> 0 0 NPARM : currently not used
> 10733 10733 NEXT : number of excluded atoms
> 129 129 NRES : number of residues
> 1025 1025 NBONA : MBONA + number of constraint bonds
> 1389 1389 NTHETA : MTHETA + number of constraint angles
> 2555 2928 NPHIA : MPHIA + number of constraint
> dihedrals <-------------------- different
> 39 41 NUMBND : number of unique bond
> types <-------------------- different
> 84 90 NUMANG : number of unique angle
> types <-------------------- different
> 40 48 NPTRA : number of unique dihedral
> types <-------------------- different
> 26 27 NATYP : number of atom types in parameter file, see
> SOLTY below <-------------------- different
> 0 0 NPHB : number of distinct 10-12 hydrogen bond pair
> types
>
>
> The pdb file (without hydrogens) and the two prmtop files are at:

http://compbio.ornl.gov/~pkc/ff02.prmtop
http://compbio.ornl.gov/~pkc/ff03.prmtop
http://compbio.ornl.gov/~pkc/pro-noh.pdb

Could someone explain me why the same protein should have different
> parameters. Specifically,
> why should the total number of dihedrals shoot up by 439 on changing the
> forcefield.
>
> Thanks.
>
>

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