AMBER Archive (2008)

Subject: Re: AMBER: seeking help regrading Zinc protein GBSA minimization

From: Carlos Simmerling (
Date: Fri Nov 28 2008 - 06:33:16 CST

I would check to see what solvation radii are being used for the Zinc,
that's like the problem since it's only used in the GB calc and not
the explicit water one. look carefully in your leap and sander outputs
for messages related to this. you might also check to see if the GB
energy is going down a lot when this happens. I recall this being
discussed before on the list, so you should check the archives. search
for zinc radii or zinc radius.

On Thu, Nov 27, 2008 at 7:32 AM, S.Sundar Raman <> wrote:
> 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
> 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
> 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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