Yes, I tried to do the same. I minimize my protein complex at different
different steepest descent method steps (like 500, 1000, 1500 , 2000, 2500
steps ) but in all cases, when I proceed to the heating step, I got stuck
with the same SHAKE error showing overlap of coordinates for two atoms. Here
I would like to mention that the protein was ok for overlap problem before
minimization.
Please let me know your feedback on this
Regards,
Hirdesh
On Sat, Jan 22, 2011 at 1:43 PM, Jason Swails <jason.swails.gmail.com>wrote:
> 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
> > > > _______________________________________________
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> > > > AMBER.ambermd.org
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> > > >
> > >
> > >
> > >
> > > --
> > > Jason M. Swails
> > > Quantum Theory Project,
> > > University of Florida
> > > Ph.D. Graduate Student
> > > 352-392-4032
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
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> > >
> > _______________________________________________
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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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sat Jan 22 2011 - 01:30:02 PST
