From: Aaron Oakley (aarono_at_uow.edu.au)
Date: Fri Jun 08 2012 - 03:23:07 CDT
In the following publication, a modified CHARMM force-field called charmm22* is described:
Piana S, Lindorff-Larsen K, Shaw DE. How robust are protein-folding simulations with respect to force field parameterization?
Biophys J. 2011 May 4;100(9):L47-9.
They claim that their new forcefield, CHARMM22*, has a much better balance of secondary structure stabiliy with respect to the existing CHARMM forcefields.
The only "edition" of CHARMM22* I have been able to find comes with the DESMOND distribution and is in a DESMOND-specific format.
The changes between the latest CHARMM and CHARMM22* are:
-modifications to partial charges on ASP, GLU and ARG.
-modification of dihedrals on ASP
-removal of CMAP correction from all residues except GLY and PRO
-modification of backbone phi and psi dihedral potentials.
Its fairly straightforward to introduce these into par_all22star_prot.inp file.
The problem occurs when I run NAMD. I get the following warnings:
Warning: IDENTICAL PERIODICITY! REPLACING OLD VALUES BY:
k=-1.825 n=1 delta=90
..and so on.
This is due to the way the phi and psi dihedrals were re-parameterised by the authors.
In charmm parameter file format they look like this:
C CT1 NH1 C 0.2000 1 0.00 ! C22STAR
C CT1 NH1 C -0.2000 2 0.00 ! C22STAR
C CT1 NH1 C -1.8250 1 90.00 ! C22STAR
C CT1 NH1 C 0.0540 2 90.00 ! C22STAR
C CT1 NH1 C -0.1090 1 150.00 ! C22STAR
C CT1 NH1 C 0.0770 2 150.00 ! C22STAR
C CT1 NH1 C -0.0960 3 150.00 ! C22STAR
C CT1 NH1 C -0.1060 4 150.00 ! C22STAR
NH1 C CT1 NH1 0.6000 1 0.00 ! C22STAR
NH1 C CT1 NH1 -2.2860 1 60.00 ! C22STAR
NH1 C CT1 NH1 -0.3620 2 60.00 ! C22STAR
NH1 C CT1 NH1 0.0130 1 150.00 ! C22STAR
NH1 C CT1 NH1 0.9420 2 150.00 ! C22STAR
NH1 C CT1 NH1 0.2670 3 150.00 ! C22STAR
NH1 C CT1 NH1 -0.1270 4 150.00 ! C22STAR
is there a workaround that can be used in NAMD?
A/Prof Aaron Oakley
School of Chemistry
University of Wollongong
Wollongong, NSW, 2522
Phone: (02) 4221 4347
Fax: (02) 4221 4287
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