Hi Hirdesh
I had the same problem, two atoms getting overlap and failure of MD run when I was
doing constant pH MD simulation.
But I think you are doing normal MD simulation, you check your PDB file generated
after tleap for protonation state and compare with amber prep file. May be problem
will be there.
Hope this work
> 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
>> > > > _______________________________________________
>> > > > 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
>> > >
>> > _______________________________________________
>> > 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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>
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Sat Jan 22 2011 - 03:00:03 PST
