Re: AMBER: Equilibration of protein complex in POPC membrane, the whole TIP3 solvated

From: Gustavo Seabra <>
Date: Wed, 28 Nov 2007 16:04:32 -0500

> Summing up all that I could learn from the literature,I guess that the system
> should be first energy minimized with protein-complex restrain (SHAKE on H
> atoms and PME). For membrane I found indications of ca. 30 kcal/molxA^2. No
> idea how that could be applied to my protein-complex.

I just want to mention that it is generally a bad idea to use SHAKE
for minimizations, since it can lead to unpredictable results.

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Dec 02 2007 - 06:07:12 PST
Custom Search