AMBER Archive (2009)

Subject: [AMBER] (no subject)

From: waleed zalloum (waleed_zalloum_at_yahoo.com)
Date: Wed Apr 29 2009 - 07:15:12 CDT

Dear Amber users,
 
I am using sander to calculate the 3D structure of a conjugate of oligopeptide and oligonucleotide. I start the calculation at 1000K. in the output file, the nucleotide bases are not planner and amino groups are distorted. My question is, how could I constrain the amino groups and the planarity of nucleotide bases?
 
Thank you
 
Waleed

      
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