You're at a local minimum for the minimization algorihtm you used! Please
check the amber website for more stuff on linmin failures. Using the
Newton Raphson minmizer (in NMODE) would get you further down, but is
not necessary for most projects.
Natasja Brooijmans
Graduate Program in Chemistry & Chemical Biology
Department of Pharmaceutical Chemistry
University of California, San Francisco
San Francisco, CA 94143-0446
phone: 415-476 8291
fax: 415-502 1411
e-mail: nbrooij_at_itsa.ucsf.edu
On Thu, 19 Dec 2002, William Wei wrote:
> Hi all,
>
> While I run my minimization on one protein. It gives me the failure message:
> RESTARTED DUE TO LINMIN FAILURE
>
> But it is after more than 20K cycles minimization. And I restart it again,
> after another 3000 cycles, sander gave me the message again. Why is that? I
> hope it is not because of the structure's clashing. I can not see any
> clashing from the structure. Could anybody give me some clue for that?
>
> Thanks a lot,
>
> William
>
> -------------------------
> William Wei
> Faculty of Pharmacy
> 19 Russell Street
> Toronto, ON. M5S 2S2
> Tel: 1-416-946-8469
> Fax: 1-416-978-8511
> Email: william_at_phm.utoronto.ca
> william.wei_at_utoronto.ca
>
>
>
>
Received on Thu Dec 19 2002 - 13:16:44 PST
