AMBER Archive (2002)

Subject: Re: LIMIN Faliure/Energies per residue for B-DNA etc.

From: darden (darden_at_gamera.niehs.nih.gov)
Date: Thu Jan 31 2002 - 15:11:19 CST

Sorry I can't help much with anal. As far as pme goes there have been some
problems with minimization failing or stalling. One of these had to do
with the nonbond list update somehow messing up conjugate gradient
minimization. Usually a subtle effect that happens after awhile. The
details of pme were designed around MD with little or no attention to
minimization, so hopefully your md experiences will be better. I think the
upcoming release of amber7 will offer a better pme/minimization module. At
least the nonbond update/conjugate gradient bug has been addressed (am I
right Dave and Mike (DAC & MFC))??
 Tom Darden
 On Thu, 31 Jan 2002, Prabal Maiti wrote:

> Dear Amber users:
> I dowloaded a PDB file for a crystal str. of B-DNA from Protein data bank
> and thorugh Leap I added Na+ ions and then solvated it. After that I ran
> minimization with PME. After 250 minimization steps it crashed saying
> "REPEATED LINMIN FAILURE". I changed the BOX dimension (make it larger) by
> hand in the prmtop file (a suggestion in the AMBER home page). But same
> things happened but after 290 steps. Any solution.
>
> Anyway I took the minimized str. after 290 minimization steps and started
> running MD with sander for 500ps.
>
> Now I want to calculate energy for each residue for the DNA and also
> want to compute the helical parameters. Is it
> possible? Looking at manual it seems I can do it by ANAL. However my
> initial try failed. So can someone send me a proper 'analin' file and also
> explain (please be explicit) how to do this.
> Thanks
> Prabal
>
>