AMBER Archive (2007)

Subject: AMBER: How to use loadpdbusingseq command to load branched structure?

From: Siang Yip (siangyip_at_gmail.com)
Date: Fri Oct 19 2007 - 12:21:36 CDT

Dear amber users,
     Nowadays I have been simulating sugar structures. The sugar structue is
branched. For example part1 = sequence { A B C D}, part2 = sequence {E F},
and the E of part2 is connected to the B of part1. Unfortunatelly it seems
that the amber could not recognize this sequence. I try loadpdbusingseq PDB
{A B C D E F}, the result is that the E is connected with D, not B. I am
wondering that how to fix this problem. 

-- 
Best Regards!
Siang Yip

=============================
Siang Yip, Ph.D.
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
Phone: (949) 824-9562
Email: siangyip_at_gmail.com
=============================

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