AMBER Archive (2004)

Subject: AMBER:

From: Xiaowei Li (
Date: Fri Mar 26 2004 - 14:21:08 CST

Hi, amber users:
Now I am suffering one question about AMBER. The
question can be described as following:
  I want to get the vibration frequencies of DNA chain. So
first step, I used nucgen in AMBER to creat pdb file of
Second, I loaded the pdb file to LEap, and LEap added
all missed H atoms to DNA chain, then I used Saveamberparm
to save DNA chain with H atoms into two files, one is
  prmtop file and another is inpcrd file.
  The third, I used following setence to calculate the
frequncies of DNA chain:
$AMBERHOME/exe/nmode -O -i -o nmdmin.out -p
  prmtop -c inpcrd -r nmd.rst
Finally, I got a wrong message said that the numbers of
  atoms in -p and -c do not agree.
This error message is unreasonable to me beause I saved
the prmtop and inpcrd file at the same time for the same
chain. I also checked the number in both files, and they
are the same. I can not go ahead without solving this
problem correctly. Thank you very much for your nice help.

  Xiaowei Li
University of Virginia
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to