AMBER Archive (2004)

Subject: AMBER:

From: Xiaowei Li (xl3a_at_cms.mail.virginia.edu)
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
DNA.
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 nmdmin.in -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.

  Best,
  Xiaowei Li
University of Virginia
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