On Tue, May 15, 2012, C.M. Baker wrote:
>
> I'm running some simulations of DNA (canonical B-form) using amber with the
> parmbsc0 parameter set. Everything seems to work fine, but I've noticed
> that I get different results depending on whether I use tleap or sleap for
> my initial system set-up.
>
> source leaprc.ff99bsc0
> dna1 = loadPdb 1BNA_no_waters.pdb
> saveAmberParm dna1 1bna_99.prmtop 1bna_99.prmcrd
At this point, you could use readparm to print and examine the dihedral
angle parameters (say esp. around delta) in the prmtop files created by
tleap and sleap. Looking at energies of the initial coordinates should
also show whether or not there are any differences that would eventually
result in different distributions of angles.
leaprc.ff99bsc0 reads in a main parameter file, followed by two frcmod
files. This leads me to suspect that the differences may arise from how
frcmod files are interpreted. One way to test this is to try sleap vs. tleap
using leaprc.ff10, which does not make use of frcmod files. Again, I'd think
that close examination of the prmtop files, or of single point energies,
should suffice; one presumably doesn't need to run converged simulations from
each option.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue May 15 2012 - 04:00:03 PDT
