Quoting simon sham <ssha...@yahoo.com>:
Hi,
Once again, I appreciate all the responses.
1. To correct I just had in the previous email. I used GROMOS53ab
not CHARMM. My apology.
2. At high temperaure, one of the helical turn in a alpha helix (3
residues) turns into a coil in GROMOS forcefield throughout the 20ns
simulation. It was only slightly distorted in OPLSAA simulation in
20ns.
3. The RMSF (backbone) for those 3 residues: 0.3nm in GROMOS vs. 0.1
nm in OPLSAA.
As I mentioned, the protein is near its melting temperature,
therefore, I am not surprised to see some helix to coil transition
or helical distortions. As Justin has suggested, I probably will try
to make a longer run to see what will happen.
Gromos96 53a6 shows a bias towards extended configurations, thus
excessively destabilizing helices. There are recent papers about this
phenomenon. Sort of a huge difference between Gromos96 and CHARMM :)
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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