AMBER Archive (2004)

Subject: Re: AMBER: why the enegy of native state of protein is high in GBSA calculation?

From: David A. Case (
Date: Fri Jun 04 2004 - 08:00:47 CDT

On Fri, Jun 04, 2004, J. Zhang, Dr wrote:

> constant temperature GBSA run
> &cntrl
> imin=0, ntb=0, ntt=1, ntc=2, ntf=2, dt=0.002, cut=8.0,

Don't use such a small cutoff for GB simulations; you should try something
on the order of 15-20 Ang.

This probably doesn't affect your energy results; see the recent post by
Carlos Simmerling. The protein folding problem would be much easier if
one could count on the native state having the lowest energy....

...good luck...dac

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