AMBER Archive (2008)

Subject: AMBER: seeking help regrading Zinc protein GBSA minimization

From: S.Sundar Raman (sundar02_at_gmail.com)
Date: Thu Nov 27 2008 - 06:32:08 CST

Dear amber friends,
I am trying to do minimization in implict solvent by GBSA method ( igb=5)
for a zinc protein complex. i used zinc and histidince force fields from
http://www.pharmacy.manchester.ac.uk/bryce/amber.
When i did the minimization and simulation in explicit environment, it goes
well. While i am trying to do GBSA minimization (200 steps) the histidine
side chain atoms moves 10A away from each other, therefore van der Waals and
bond energy reached unprintable limits. I would like to know how to do GBSA
or PBSA minimization and simulation for zinc-protein complex.
i am eagerly waiting for reply. 

-- 
S.Sundar Raman
CSIR-SRF
Chemical Laboratory
Central Leather Research Institute
Adyar, Chennai, India- 600 020
       &
DAAD Research Scholar
Hause No. 5, Room No. 106
Ulmenweg 55, Mannheim, Germany - 68167

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