Greetings:
I am trying to do cluster analysis. I used ptraj to create a coordinate file
with only 50 frames without waters. Then I created a topology file
without waters. I used the no water topology and coordinate files to
cluster. The representative cluster pdb files were created however I
encounter an error that reads: Failed on when looking for box coordinates;
Too many iterations in routine JACOBI. I am not sure why this is happening.
Any suggestions? Thanks
On Sun, Jun 13, 2010 at 9:44 AM, Jason Swails <jason.swails.gmail.com>wrote:
> It could certainly be reasonable if the two simulations sampled different
> regions of phase space. One thing that may help you decide one way or the
> other is to do a decomposition analysis and see which residues changed the
> most, then take a look at how those specific residues behave throughout the
> course of each simulation. That is, of course, if no large-scale
> conformational differences between the 2 can be discovered by quickly
> comparing the trajectories. Keep in mind that just because 2 structures
> have an RMS of 2.5 A from a common structure does not mean that they are
> identical themselves.
>
> Good luck!
> Jason
>
> On Sun, Jun 13, 2010 at 11:20 AM, Catein Catherine
> <askamber23.hotmail.com>wrote:
>
> >
> > Dear Sir/Madam,
> >
> >
> >
> > I did a calculation twice, each 10 ns, start with the same prmtop and
> > inpcrd files. Both systems comes to a constant ETOT energy after 2ns.
> RMSD
> > less than 2.5A and become stable after 2ns.
> >
> >
> >
> > However, I found the results from the two runs are different.
> >
> >
> >
> > Then, I do the GBSA analysis. I found the MM/GBSA total energies are
> > different by ~6 kcal/mol.
> >
> >
> >
> > Could you mind to share your experience with me if it is a reasonable
> > results?
> >
> >
> >
> > Best regards,
> >
> >
> >
> > Cat
> >
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>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
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Shenna
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Received on Fri Jun 25 2010 - 09:00:03 PDT
