Dear Amber users and developers,
I have 3 systems with different phosphorylation sites. I am interested in
secondary structure analyses of these systems. I am using ff10 force field
with tip3p potential. I started conventional MD with disordered structure
and after equilibration, ran production for 50ns (NPT) followed by aMD
(accelerated MD- dual boost potential as implemented in AMBER12.2 GPU
version) runs upto 300ns.
I also performed conventional MD for 1 microseconds (same force field and
ensemble as above) which showed that system (1) presence of helical
structure in the centre; systems (2) and (3) had beta sheets at the N- and
C-terminals and no helical structure. These analyses from the trajectories
agree with the experimental data.
The secondary structure analyses obtained from the aMD runs show that all 3
systems have similar helical structure for last 50 ns. These doesn't
correlate with experimental data.
How do I interpret these aMD results? What could be the other parameters
which could be looked that? Does aMD has preference for helical structures
or is the force field?
Your help is appreciated,
--
Regards,
Dr. Neha S. Gandhi,
Curtin Research Fellow,
School of Biomedical Sciences,
Curtin University,
Perth GPO U1987
Australia
LinkedIn
Research Gate
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Apr 12 2013 - 06:30:02 PDT
