Hi,
Thanks Jason for your reply. No there was nothing written like Stderr in the
output file.. Even there is no warning as well in mdout file. It just have
minimization information upto steepest descent method.
Hirdesh
On Thu, Jan 20, 2011 at 7:20 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Thu, Jan 20, 2011 at 12:58 AM, Hirdesh Kumar <hirdesh.iitd.gmail.com
> >wrote:
>
> > Hi Amber Users,
> > I am doing MD of my protein bound with ligand and cofactor. The complex
> was
> > prepared well using antechamber and tleap modules (did not show any
> > error).*TIP3P
> > * water type was used to solvate the system. I minimized the protein
> > complex
> > (*total :5320 atoms*) using steepest descent and conjugate gradient
> method
> > (
> > *Total: 2500 and ncyc:1500*). It showed "Linmin Error" when it moved from
> > steepest descent to conjugate gradient. I searched for the error and
> found
> > it to be related to some coordinate overlap. To solve the problem, I
> >
>
> This does not seem right to me (although maybe that can cause it to
> happen...) LINMIN failures simply imply that the minimizer got stuck and
> couldn't figure out how to find its way "downhill". If you've hit this
> point in the minimization, then you are typically fine to start MD if
> that's
> what you're aiming for. If you're really trying to find a *good* minimum,
> then consider using the xmin minimizer (see the Amber manual, specifically
> setting ntmin=3). Here's a page with more information
> http://ambermd.org/Questions/linmin.html .
>
>
> > optimize my complex using Schrodinger and again prepare the protein
> complex
> > using tleap. This time it is not showing such error (no warning in the
> > mdout
> > file) but still the job was killed at 1500 step. In mdout file also it is
> > not showing any warning.
> >
>
> Was anything written to stderr?
>
> Good luck!
> Jason
>
>
> >
> > I am confused whether I should ignore this and optimize my system using
> > increased number of steepest descent minimization and no conjugate
> gradient
> > steps? Suggest me what should I do?
> >
> > Thanks,
> > Hirdesh
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
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>
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Received on Thu Jan 20 2011 - 20:30:06 PST
