AMBER Archive (2007)

Subject: AMBER: protein-rna interaction & mmpbsa

From: Antonio Morreale (amorreale_at_cbm.uam.es)
Date: Thu Apr 26 2007 - 03:28:19 CDT

Dear members,

I am trying to obtain the interaction energy between a protein and rna
strand using mm_pbsa.pl script. Once that the trajectory has been
performed, the output from mm_pbsa.pl script showed no cancelation of
the internal energy. I have been doing many calculations for
protein-ligand interaction without this problem. Also, the ras-raf
example shows a cancelation of this term. Any hint on this?

Thanks in advance.
Antonio 

-- 
Antonio Morreale
Unidad de Bioinformática
Centro de Biologia Molecular "Severo Ochoa"
Universidad Autonoma de Madrid
Cantoblanco, 28049 Madrid (Spain)
Phone: (34) 91-497-2377
Fax:   (34) 91-397-4799
e-mail: amorreale_at_cbm.uam.es
web: http://ub.cbm.uam.es/

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