Re: [AMBER] ptraj and ambpdb problem in Amber Tools 1.4

From: Thomas Cheatham III <>
Date: Mon, 22 Nov 2010 12:34:20 -0700 (Mountain Standard Time)

> I used tleap as follows:
> > AddAtomTypes { {"K+" "K" "sp3"} {"Cl" "Cl" "sp3"} }
> > loadOff /usr/local/amber11//dat/leap/lib/ions08.lib
> > loadAmberParams /usr/local/amber11/dat/leap/parm/frcmod.ionsjc_tip3p
> > rna = loadPdb triNucTest.p
> > addIons rna K+ 3 Cl- 1
> > saveAmberParm rna tNtest1.lcrd
> > quit
> When I used either ambpdb or a ptraj script with Amber Tools (v 1.4), the pdb file created listed the ions as follows:
> ATOM 96 K+ K+ 4 4.125 -8.386 -13.629 1.0000 1.5000

There are two type of radii in the prmtop; the Lennard-Jones radius vs.
radii for implicit solvent... When dumping charge/radii to PDB files (for
example with the -pqr option to ambpdb), the implicit solvent radii are
dumped, not the Lennard-Jones radii...

The Joung/Cheatham ion parameters are for explicit solvent and represent
the Lennard Jones radii. To see these values most easily, loadup the
prmtop into "rdparm" and use the "printtypes" command.

rdparm prmtop

NOTE: if either A or C is zero (*), we cannot infer
the value of r* or epsilon and assume zero...

  Type r* eps
* HO 0.0000 0.0000
   OH 1.7210 0.2104
   CT 1.9080 0.1094
   K 1.7050 0.1937
   OW 1.7683 0.1520
* HW 0.0000 0.0000

If what you want actually are radii for implicit solvent, the Joung/
Cheatham values likely will not produce the correct dGsolvation; the
values need to be significantly altered to get the correct dGsolvation
from your chosen implicit solvent model in MM-PBSA. We did this back in
Stefl et al. Biophys. J. 85, 1787-1804 (2003); essentially, we tweaked the
radii to get closer to the correct dGsolvation with the applied implicit
solvent model.


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Received on Mon Nov 22 2010 - 12:00:03 PST
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