AMBER Archive (2005)

Subject: AMBER: On the role of neutralizing ions in GB-MD and GBSA

From: Wu Yingliang (wuyliang_at_public.wh.hb.cn)
Date: Thu Apr 21 2005 - 05:16:29 CDT

Dear All,

I have two questions, and expect eagerly help.

(1) The effect of neutralizing ions on GB-MD

My GB-MD (IGB=2 in Amber 7) system has two different proteins. In order to neutralize this system, 7 Cl- ions was added. These Cl- ions are located in different positions instead of a straight line. After producing corresponding complex.top and complex.crd files, the system energy minimization was done as following:

sander -O -i tsem.in -o complex.out -p complex.top -c complex.crd -r complex_min.restrt -ref complex.crd

However my system can not run by wrong message "bad atom type: IM". When I do not neutralize the system without 7 Cl- ions, the energy minimization runs OK. May I know how to run my GB simulations?

I can not find clear answers about the the effect of neutralizing ions on GB-MD in AMBER Archive. Here, how about the difference of GB-MD results with/without neutralizing ions? It is essential to neutralize system in GB simulations?

(2) The effect of neutralizing ions on interactive energy

When running my or other protein-protein systems by GB (IGB=2 in Amber 7) simulations with/without neutralizing ions, respectively, how about the difference of electrostatic energy, van der Waals energy, and other energy values that are calculated by MM-GBSA? It is also essential to include neutralizing ions in MM-GBSA?

Looking forward to help, and thanks a lot in advance!

Best wishes,

Yingliang Wu

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