AMBER Archive (2007)

Subject: AMBER: AMBER sander

From: Eduardo Mendez (pckboy_at_gmail.com)
Date: Fri Sep 14 2007 - 18:42:38 CDT

I have to quickie questions. I can not tell how to solve these issues
from the manual :(

a) Can I save the final configuration on PDB format after a sander
simulation?. How?.
If you tell me I have to save the

b) I want to simulate a protein in water, but would like to combine
implicit/explicit method. should I try to put constrains in the
waters so these dont swim away from the surface of the protein?. ( I
need to see if a water enters a cavity).
Is it reasonable to mix explitic/implicit this way?

I'd appreciate any feedback I can get.

Thank you!

Eduardo
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu