Hi All,
I performed some mm-pbsa calculations on my protein-ligand system (ligand is
a small organic molecule) of ~3700 atoms .The MD was run on the solvated
system for 2ns post 1000 steps of minimization (the system gets equilibrated
after 400ps), such 4 other systems have been subjected to post-MD mm-pbsa
calculations.
I am worried about the huge TSVIB standard deviation for all the nmode
calculations, I don't believe that such a large STD makes the results
reliable. Also, as this influences the TSTOTAL, which always seems to be
more negative than the PBTOT resulting in a positive deltaG-bind.I get
similar high STDs for the other four calculations as well!
I generated snapshots from the last 200ps with NFREQ=20, hence the nmode
calculations were done over 11 snapshots. I tried genearting snapshots from
a smaller timeframe such as 50ps with NFREQ=10 to generate 6 snapshots, but
the problem persists.
# COMPLEX RECEPTOR LIGAND
# ----------------------- -----------------------
-----------------------
# MEAN STD MEAN STD
MEAN STD
# ======================= =======================
=======================
TSTRA 17.47 0.00 17.46 0.00 13.73
0.00
TSROT 17.82 0.00 17.81 0.01 11.64
0.05
TSVIB 2753.67 2.69 2739.67 18.12 34.60
0.52
TSTOT 2788.96 2.69 2774.93 18.12 59.96
0.52
# DELTA
# -----------------------
# MEAN STD
# =======================
TSTRA -13.71 0.00
TSROT -11.63 0.05
TSVIB -20.60 20.13
TSTOT -45.93 20.13
~
My NMode script is :
ismem 1
DIELC 4
t 310
MAXCYC 1000
DRMS 0.1
Thanks in advance.
Any ideas or suggestions on this?
--
-Rima
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Feb 18 2007 - 06:07:38 PST
