Hello Steven,
I follow Amber tutorial
http://ambermd.org/tutorials/advanced/tutorial25/section4.htm
Namely, I use:
gistpp -i gist-gO.dx -i2 system.pdb -op defbp -opt cutoff1 3.5 -o
system_3.5A.dx
Followed by other steps from the tutorial.
I use GIST box that completely covers the initial conformation of the
flexible peptide and should be big enough to cover the alternative
conformations.
I define 3.5 A cutoff based on the initial conformation of the flexible
peptide but it moves during the simulation. It seems that this was a
problem.
I tried increase [-opt cutoff1] from 3.5 A to 5 A and it solved a problem.
Now I get more favourable dE for the frozen peptide.
Thank you very much for your help. Thanks to you I solved the problem!
On Wed, Nov 11, 2015 at 6:33 PM, Steven Ramsey <vpsramsey.gmail.com> wrote:
> Hello Yulian,
>
> I think it would be really helpful if we knew exactly how you are
> determining dE, dS, etc. In particular how the volume around the
> configurations is defined.
>
> My first guess would be that if the total number of voxels being compared
> between rigid and flexible is the same then said volume may not encompass
> 3.5 A around all flexible configurations (which might explain an unexpected
> difference in dE).
>
> If the system is not rotating and translating it's possible to compare
> solvation by GIST without clustering, but it might require cleverly
> defining the box/volume of integration. Always happy to help,
>
> --Steve
>
> On Wed, Nov 11, 2015 at 7:21 AM, Yulian Gavrilov <zzeppelin87.gmail.com>
> wrote:
>
> > Dear Steven and Jonathan,
> >
> > Thank you for your suggestions.
> > Please note that N and C terminals of the flexible peptide are fixed in
> the
> > space, so there are no rotations/translations of the whole peptide.
> > When I analyze the first hydration shell (3.5A) around my rigid and
> > flexible peptides I noticed strange results for dE.
> > In principle, for the flexible peptide dE of the hydration water should
> be
> > less favourable than for the frozen one (opposite to dS).
> > I see it for the average value [kcal/mol per non-zero voxel] but in case
> of
> > summation [kcal/mol for all hydration shell] dE is more favourable in
> case
> > of the frozen peptide, which is strange.
> > I expected that this may be because of some 'bad' voxels but I didn't
> find
> > 'very bad' voxels in the flexible systems (with energies > 0 kcal/mol).
> > Probably it is related to the fact that the number of non-zero voxels
> > within the hydration shell is ~twice bigger for the flexible peptide (the
> > total number of voxels is identical).
> > Interesting, that for dS everything is fine (dS of water around the
> > flexible peptide is more favourable).
> > It seems that in order to make a correct comparison of the flexible and
> > rigid peptides I need to use something like clustering.
> >
> >
> >
> >
> > On Tue, Nov 10, 2015 at 5:28 PM, Jonathan Gough <
> > jonathan.d.gough.gmail.com>
> > wrote:
> >
> > > Hi Yulian Gavrilov,
> > >
> > > What Steve said is spot on. In the present implementation of
> > gist-cpptraj,
> > > the energy calculations utilize the periodic box dimensions (I believe
> > it's
> > > from the first frame) when calculating energy. When one uses the
> cpptraj
> > > rms function the entire box is rotated at every frame. Therefore the
> > change
> > > in box position is lost. As a result the energy calculations are all
> > wrong.
> > >
> > > How were you planning on calculating the desired values(dA, dTS, dE)?
> > >
> > > If you can simply calculate the values by integrating over the entire
> box
> > > volume, you could run the simulation restrained and unrestrained. Then,
> > > make your gist box large enough (probably best to do the same/identical
> > > size about both simulations) to encompass the peptide and run gist.
> Then
> > > you could utilize the post processing tool, gistpp, to get the values
> you
> > > wish for each system and then compare.
> > >
> > > you can find the instructions for gistpp on the last page of the
> > tutorial:
> > >
> > > http://ambermd.org/tutorials/advanced/tutorial25/section4.htm
> > >
> > >
> > > You can grab the code from the above page or from github.
> > >
> > > https://github.com/gosldorf/gist-post-processing
> > >
> > > Don't hesitate to reach out if you need additional help.
> > >
> > > Best,
> > > Jonathan
> > >
> > >
> > > On Tue, Nov 10, 2015 at 10:04 AM, Steven Ramsey <vpsramsey.gmail.com>
> > > wrote:
> > >
> > > > You can certainly analyze solvent properties around a flexible
> system,
> > > > however there are some things to keep in mind:
> > > >
> > > > The GIST grid itself will not move with your system (neither will
> each
> > > > individual voxel), therefore the sampling in certain voxels,
> > particularly
> > > > those that are near your solute, will have lower sampling due to
> solute
> > > > fluctuations, which may effect several quantities (g(O), S, E).
> > > >
> > > > You could align the flexible system (or cluster it as you suggested),
> > but
> > > > then this may introduce another potential issue which was brought up
> in
> > > > this thread:
> > > >
> > > > http://archive.ambermd.org/201508/0149.html
> > > >
> > > > Entropy should be fine on a clustered system, provided there's enough
> > > > frames to sample from. The lesser populated clusters may produce
> > > > thermodynamics that are not-trustworthy (meaning not converged, but
> > that
> > > > applies to all quantities not just S).
> > > >
> > > > So to summarize a bit, it is definitely possible to analyze a
> flexible
> > > > system, but it is more troublesome than a rigid one. A lot depends on
> > > just
> > > > how flexible it is. Either choice (running GIST on a flexible
> > simulation
> > > or
> > > > a clustered one) will map solvation data to the defined voxels, so
> you
> > > can
> > > > potentially play around with it and see what works for your system.
> > > >
> > > > Hope this helps,
> > > >
> > > > --Steven Ramsey
> > > >
> > > >
> > > > On Tue, Nov 10, 2015 at 3:24 AM, Yulian Gavrilov <
> > zzeppelin87.gmail.com>
> > > > wrote:
> > > >
> > > > > Dear all,
> > > > >
> > > > > I have a question about GIST.
> > > > >
> > > > > In the tutorial and manual it is written that the protein should be
> > > rigid
> > > > > in order to use GIST to analyze water around it.
> > > > >
> > > > > Is there any way to analyze hydration water around a flexible
> > molecule?
> > > > > I would like to compare the thermodynamic parameters (dA, dTS, dE)
> of
> > > > > hydration water around the flexible and rigid version of a peptide.
> > Is
> > > > > there any way to do it?
> > > > > I use AmberTools15.
> > > > >
> > > > > Only idea that I have is to devide the output trajectory of the
> > > flexible
> > > > > peptide into several clusters based on RMSD, so that within the
> > cluster
> > > > the
> > > > > flexibility of a peptide will be minimal. Then I can use GIST for
> > each
> > > > > cluster separately. But this way I won't get the right entropy
> > values,
> > > > > right?
> > > > >
> > > > > Thank you in advance for any ideas!
> > > > >
> > > > >
> > > > > --
> > > > >
> > > > > Sincerely,
> > > > >
> > > > > Yulian Gavrilov
> > > > > _______________________________________________
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> >
> >
> >
> > --
> >
> > Sincerely,
> >
> > Yulian Gavrilov
> > _______________________________________________
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> >
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--
Sincerely,
Yulian Gavrilov
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Received on Thu Nov 12 2015 - 01:30:04 PST
