I wish to use the ion parameters of Joung & Cheatham with RNA. I believe they have been loaded properly in the topology file but ptraj and ambpdb of AmberTools give the wrong ionic radii.
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.top 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
ATOM 97 Cl- Cl- 5 0.125 -7.386 -14.629 -1.0000 1.5000
ATOM 98 K+ K+ 6 1.125 -6.386 -18.629 1.0000 1.5000
ATOM 99 K+ K+ 7 17.125 -9.386 -10.629 1.0000 1.5000
Tese are the radii from ions94. When I used the same topology and coordinate files but used ptraj from Amber9 I got the following ion listing:
ATOM 96 K+ K+ 4 4.125 -8.386 -13.629 1.0000 1.7050
ATOM 97 Cl- Cl- 5 0.125 -7.386 -14.629 -1.0000 2.5130
ATOM 98 K+ K+ 6 1.125 -6.386 -18.629 1.0000 1.7050
ATOM 99 K+ K+ 7 17.125 -9.386 -10.629 1.0000 1.7050
These are the expected ionic radii. Is this a problem in AmberTools? Is PMEMD of Amber11 using the new ion parameters?
Mike Bruist
Dr. Michael F. Bruist
Associate Professor of Biochemistry
Department of Chemistry & Biochemistry
Griffith Hall 147
University of the Sciences in Philadelphia
Philadelphia, PA 19104-4495
Phone (Office & Voice Mail): (215) 596-8530
Department Phone: -8839
Department Fax: -8543
E-mail: m.bruist .usp.edu
web page: http://tonga.usp.edu/bruist
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Received on Mon Nov 22 2010 - 11:30:03 PST
