Dear Amber Users:
I have minimized my apo protein in the following step
500 step (protein restrain 25 ) ion & WAT free
500 step (protein + ion restrain 25, 20 ) WAT free
100 step (protein + ion restrain 20, 15 ) WAT free
100 step (protein + ion restrain 15, 10 ) WAT free
100 step (protein + ion restrain 10, 5 ) WAT free
100 step (protein + ion restrain 5, ) ion, WAT free
500 step (Unrestrain system )
above mentioned steps are right
and
what
I got following results for 500 Unrestrained system minimization
VDWAALS = 182243.53 EEL = -1350322.29
1-4 VDW = 2143.80 1-4 EEL = 22795.94
should I increase the minimization step for these high value of VDW and EEL
Thanks in advance
Muhammad Tahir Ayub
Junior Research Fellow
Lab No. P-133, Computational Chemistry Unit,
Dr. Panjwani Center for Molecular Medicine and Drug Research,
International Center for Chemical and Biological Sciences,
University of Karachi-75270.
Karachi-Pakistan.
UAN: (92-21) 111-222-292 Ext. (309)
E-mail: tahirgp0.gmail.com
http://sites.google.com/site/zaheerqasmi/groupmember
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Received on Mon Nov 09 2015 - 22:30:03 PST
