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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> > 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 Sat Jan 22 2011 - 00:30:02 PST
