AMBER Archive (2004)

Subject: Re: AMBER:

From: David A. Case (
Date: Fri Mar 26 2004 - 15:41:32 CST

On Fri, Mar 26, 2004, Xiaowei Li wrote:

> 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 -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.

Please see bugfix.48 for Amber 7. The workaround (if you don't want to apply
the bugfix) is to carry out the minimization first in sander, then use nmode.
Running minimization first in sander is probably in any event a recommended

...good luck....dac


================================================================== David A. Case | e-mail: Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | home page: La Jolla CA 92037 USA | ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to