I believe I posted on this recently. A linmin failure simply means that the
minimizer got stuck and couldn't find its way out. If you're just starting
dynamics, you can take the structure before it hits the LINMIN failure and
run dynamics with it.
You don't need many minimization steps to relieve bad contacts.
Hope this helps,
Jason
On Sat, Jan 22, 2011 at 3:05 AM, Hirdesh Kumar <hirdesh.iitd.gmail.com>wrote:
> Hi Jason,
> Thanks for your reply. I minimized my system after preparation in
> antichamber and tleap. It showed "Linmin failure". I googled the term and
> came to know, just increase the number of steepest descent minimization
> steps and removed the conjugate gradient steps from the minimization study.
> Thus generated file i took further for heating the system.
>
> Hirdesh
>
> On Sat, Jan 22, 2011 at 12:44 PM, Jason Swails <jason.swails.gmail.com
> >wrote:
>
> > Hello,
> >
> > You should run a short minimization on your system before you try to run
> > any
> > molecular dynamics. This is the best way to relieve these bad contacts.
> >
> > After that, you should carefully heat up your system before running your
> > production dynamics.
> >
> > I hope this helps,
> > Jason
> >
> > On Sat, Jan 22, 2011 at 1:34 AM, Hirdesh Kumar <hirdesh.iitd.gmail.com
> > >wrote:
> >
> > > Hi Amber Users,
> > > I am trying to heat my protein ligand complex at constant volume. But
> it
> > is
> > > showing SHAKE error. I googled the error and found that it is due to
> > > overlap
> > > of the coordinate. I tested the same using ptraj close contact utility.
> I
> > > generated the .pdb file from the .parm7 and .rst file and change the
> > > coordinate of overlapping hydrogen. But Now I am stuck how to convert
> my
> > > protein (*.pdb format*) back into the .parm7 and .crd file. One option
> is
> > > by
> > > using tleap again on my complex, but for that I need the parameter file
> > for
> > > my solvent molecule (i.e. TIP3P). Is there any other option for the
> > same??
> > >
> > > Thanks and Regard,
> > > Hirdesh
> > > _______________________________________________
> > > AMBER mailing list
> > > 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sat Jan 22 2011 - 00:30:03 PST
