AMBER Archive (2005)

Subject: Re: AMBER: minimizing structures before MM-PBSA?

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Tue Feb 22 2005 - 19:37:18 CST

you should not need to do this- why would a snapshot from MD
have "bad contacts"? is the MD stable, with reasonable temperature, etc?
these snapshots (if the MD is ok) should be good, clean structures
for that system, with no more than thermal fluctuations. I guess it's
possible that you might need to minimize but I would look carefully
at the dynamics first to see why the problem is there. perhaps you
did not equilibrate the system well enough to remove bad contacts
from your initial structure?

scopio wrote:

> Dear Amber Users:
>
> When I do mm-pbsa calculations, I find some generated snapshots are
> not very clean and sometimes have bad contacts. I'm wondering if
> it's necessary to minimize all the complex structures before
> generating snapshots for mm-pbsa calculations?
>
> Best!
>
> Liu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu