AMBER Archive (2006)

Subject: AMBER:

From: emilia wu (
Date: Mon Mar 20 2006 - 06:38:17 CST

dear all,

i came cross a problem which confuse me for several days. i am studing the bingding of a protein and ligand with MMPBSA.
but i found something is wrong with my result of entropy. i copy a part of my output file here.

# -----------------------
# =======================
TSTRA -13.50 0.00
TSROT -11.38 0.02
TSVIB 1.83 8.95
TSTOT -23.05 8.97

i am wondering why the value of TSVIB is positive, and what this means? i think it should be negative just from the
physical intuition. is it means my parameters of ligand is not accurate?

i am very apprciate for any suggestions !
thanks in avdance!

        emilia wu
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to