From: Xiaowei Li <>
Date: Fri, 26 Mar 2004 22:53:54 -0500

Thank you very much, I will run Sander first and then
Nmode. I think your aswer is correct solution to my

Xiaowei Li
University of Virginia

On Fri, 26 Mar 2004 13:41:32 -0800
  "David A. Case" <> wrote:
>On Fri, Mar 26, 2004, Xiaowei Li wrote:
>> I want to get the vibration frequencies of DNA chain.
>> 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
>> 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 |
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Received on Sat Mar 27 2004 - 04:53:01 PST
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