Subject: CMC/MD Help!

From: William Wei <[email-masked]>
Date: Fri, 30 Nov 2001 12:41:25 -0500

Dear friends:

I am trying to perform CMC/MD on my protein/inhibitor(s) system.  I met
some problems with it. I have read the paper 1 and 3 that amber manual
gives. I can not find the second reference. Could anyone give me a copy
of that reference?

There is little guide for how to use the program Sander.MC, even the
useage of this package, is it the same options and parameters with
mender? and what is contents in the file MCFIL?

Another question is where the result of the Free Energy Changes in the
output file? I have noticed there is a part in the output file:
---------- MC summary ----------
    2    5    2
MC res:     2 counts:        260 partition:         0.7416554555
MC res:     3 counts:          0 partition:         0.2098557652
MC res:     4 counts:          0 partition:         0.0484887793
MC res:     5 counts:          0 partition:         0.0000000000
---------- MC summary ----------       260

are the partitions the Pi(s) mentioned in reference 3? if they are, are
the Pi(s) accumulated and scaled? Can I use it to caculate the Delta
delta Gbind (=-RTln(Pj/Pi)? Please forgive me for the naive question.
Any hints and reply is appreciated. Thank you very much and have a nice
weekend.

William.

--
William Wei                    Tel: 1-416-946-7551 (Lab.)
Faculty of Pharmacy            Fax: 1-416-978-8511
19 Russell Street              Email: [email-masked]
Toronto, ON. M5S 2S2, Canada          [email-masked]