AMBER Archive (2006)

Subject: AMBER: Nucgen Problem

From: puneet kacker (puneet_bioinfo_at_yahoo.com)
Date: Fri Dec 22 2006 - 02:06:41 CST

Dear

I am unable to generate a dsDNA by nucgen command.
Usually it generates two files, a .out file and a .pdb
file. While on my system nucgen is generating both the
files but there is no coordinates(0 bytes) for the
molecule in the nuc.pdb file however the file nuc.out
is generating without any error.
The command which I am using is as follows-
 
nucgen -O -i nuc.in -o nuc.out -d Path_for_nucgen.dat
-p nuc.pdb

The file format of nuc.in is exactly as mention in a
tutorial of Ross Walker.
 
Any kind of help will be highly appreciated.

Thanks
Puneet

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