AMBER Archive (2005)

Subject: Re: AMBER: Is the MD simulation normal

From: Shulin Zhuang (shulin.zhuang_at_gmail.com)
Date: Fri May 27 2005 - 02:38:05 CDT

Dear Prof. Duan,

I have ever MD of one inhibitor with a Ki of only 2.33mM, but all goes
well, what's more the the inhibitor binds to the same protein with the
disccussed inhibitor that has IC50 of 7uM. The big difference is that,
the former inhibitor is very rigid and the later is relatively
flexable and has 30 atoms.

according to your advice, I get the B-factor of the inhibitor,
B-factors of several atoms are too big. Does it means that the results
are normal and I need not to continue to run the MD?

Please see the following data:

Atom no B-factor

1 4.8025
2 32.48008
3 27.58063
4 28.61952
5 2.31655
6 2.37586
7 11.6511
8 2.62466
9 4.47218
10 7.26247
11 2.72919
12 4.15794
13 6.45167
14 6.92309
15 4.71467
16 5.09964
17 3.57848
18 2.85317
19 1.01439
20 1.39801
21 3.13097
22 2.43842
23 5.56094
24 2.49007
25 7.00789
26 10.12751
27 1.14021
28 2.71137
29 0.81603
30 2.5196

best regards
shulin 

-- 
   Shulin Zhuang
Chemistry Department 
Zhejiang University PRC
shulin.zhuang_at_gmail.com
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