AMBER Archive (2005)

Subject: AMBER: nucgen error (U not generated)

From: mathew k varghese (mathew_kvarghese_at_yahoo.co.in)
Date: Wed Jul 27 2005 - 22:28:51 CDT


DearAMBER users,

I have used nucgen to create an ARNA. My input file is

-------------------------------------------------------
 NUC 1
D
G5 C C A C C C U G3
                       
                                                      
                         
  NUC 2
D
C5 A G G G U G G C3
                       
                                                      
                         
END
                         
$ARNA
-------------------------------------------------------
The nucgen program runs without any error message and
creates the RNA molecule.But the created molecule
doesnot have the uracil bases. The U residue contains
only the sugar and phosphate. What is wrong ith my
input?
Thanking you,
Mathew

/\/\athew

Mathew K Varghese
Research Scholar
School of Pure and Applied Physics
M.G.University
Kottayam, Kerala
India

email mathew_kvarghese_at_yahoo.co.in

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