On Tue, Jun 10, 2003, Javier Cuervo wrote:
>
> I got the following message when I am trying to do a minimization( with
> amber7):
>
> .... RESTARTED DUE TO LINMIN FAILURE ...
>
> FINAL RESULTS
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1273 -7.8756E+03 7.5693E-03 1.8686E-01 NH2 2774
> ... [the rest of the usual information]
>
> ***** REPEATED LINMIN FAILURE *****
>
> The input file I am using is the following:
>
> minimize structure
> &cntrl
> imin=1, maxcyc=10000,
> cut=300.0, igb=2, gbsa=1,
> ntpr=10, ntx=1, ntb=0,
> &end
There are places in the surface area algorithm where the derivatives are
not completely smooth, and this prevents the minimization algorithm from
getting to really low gradients.
>
> The RMS is ~7 exp-3, wich is close the default threshold for stoping
> criteria (1x10-4), will be ok take this coordinates and do the
> equilibration regardless the error given by sander?
Absolutely. Generally, on a few hundred steps of minimization are needed
before equilibration. With "good" initial structures, you might not need
minimization at all. If you goal is to run MD anyway, don't waste unnecessary
time on minimizations.
...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
==================================================================
Received on Wed Jun 11 2003 - 07:53:01 PDT
