Thank you very much, I will run Sander first and then
Nmode. I think your aswer is correct solution to my
question.
Best,
Xiaowei Li
University of Virginia
On Fri, 26 Mar 2004 13:41:32 -0800
"David A. Case" <case.scripps.edu> wrote:
>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 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.
>
>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
>procedure.
>
>...good luck....dac
>
>--
>
>==================================================================
>David A. Case | e-mail:
> case.scripps.edu
>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 |
> http://www.scripps.edu/case
>==================================================================
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Received on Sat Mar 27 2004 - 04:53:01 PST
