On Tue, Apr 30, 2002, X. Tan wrote:
>
> I tried to follow the tutorial of biotin to do MD simulation with cap
> water, but I got the following message when run minimization.
>
> -------------------------------------------------------
> Amber 6 SANDER Scripps/UCSF 1999
> -------------------------------------------------------
You are supposed to use sander_classic (not sander) to run this tutorial.
If you want to try sander, you will have to set ntb=0 in the input file,
in order to tell the program that you do not have a periodic system.
(ntb=0 is the default in sander_classic, but ntb=1 is the default in
sander).
There are probably other changes that would be required if you were to use
sander, as well....
...hope this helps...dac
--
==================================================================
David A. Case | e-mail: case_at_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
==================================================================
Received on Wed May 01 2002 - 09:10:36 PDT
