I think I understand the point Carlos mentioned.
I'm getting meaningful continuum solvation energy differences after
stripping the water and ions.
But I'm still trying to understand if there's some way to estimate the
differences in solvent and protein reorganization energies between two
states with just one charge difference using the explicit solvent MD
trajectories.
Looking forward to receiving valuable suggestions and advice from the list.
Thanks for the valuable suggestions and comments.
Best regards.
On Sat, Oct 3, 2020, 18:46 Carlos Simmerling <carlos.simmerling.gmail.com>
wrote:
> In general, molecular mechanics absolute energies cannot be compared for
> different molecules or systems. The zero is arbitrary and only relative
> energies of a given system are meaningful. The conformations sampling can
> be compared, using the methods discussed earlier in this thread.
>
> On Fri, Oct 2, 2020, 5:12 PM Vaibhav Dixit <vaibhavadixit.gmail.com>
> wrote:
>
> > Dear all,
> > This is troubling since it seems to kill the very purpose for which I
> > started to build the two states for the system.
> > Moreover the assumption that they have equal number of water molecules
> also
> > seems incorrect because while adding the extra ion to neutralize the
> system
> > tleap must have removed some water molecules that are present in the
> > trajectory.
> >
> > I think it is possible to add equal number of ions in both the systems.
> > That will keep the number of water molecules also same and make the
> energy
> > comparable. But I'm not sure if I it is meaningful to simulate a system
> > with net 1 negative charge. Will it create instabilities during the MD
> > simulations? Are sander and pmemd and other tools expected to handle this
> > correctly? I think so but can someone please confirm.
> >
> > Please suggest and help me decide the best possible way to simulate the
> > charge difference and the estimate difference in other measurable
> > properties.
> >
> > Thank you and best regards.
> > Vaibhav
> >
> > On Fri, Oct 2, 2020, 22:01 Carlos Simmerling <
> carlos.simmerling.gmail.com>
> > wrote:
> >
> > > I'm not sure I see a way to compare energies, the extra ion will
> interact
> > > with everything else due to PME, and if you delete it you'll have a
> hole
> > > that the other system won't have that likely will shift the energies
> for
> > > the water. You could strip all water and ions and compare energies in a
> > > continuum model, but you'd need to decide if that approximation is ok
> or
> > > not.
> > > maybe others have better ideas here...
> > > carlos
> > >
> > > On Fri, Oct 2, 2020 at 11:42 AM Vaibhav Dixit <vaibhavadixit.gmail.com
> >
> > > wrote:
> > >
> > > > Dear All,
> > > > these are helpful suggestions, thanks Carlos,
> > > > After these commands, I assume that, if I load the trajectory for
> the
> > > 2nd
> > > > structure and give similar rmsd commands, I should be able to see how
> > it
> > > > evolves during MD simulation, right? Then I hope I can see/compare
> them
> > > in
> > > > one plot may be using gnuplot (xmgrace is not working on my Centos
> 7).
> > > >
> > > > How can I handle this incompatibility between prmtops while
> estimating
> > > the
> > > > Es with imin=5 of one structure with parameters for the other
> > (parameters
> > > > are different only for the co-factor and residues coordinating with
> it
> > in
> > > > addition to the difference of the extra ion)?
> > > >
> > > > I hope that these questions are meaningful and I'll get valuable
> > > > suggestions to tackle the same.
> > > >
> > > > Thank you and best regards :)
> > > > Vaibhav
> > > >
> > > > On Fri, Oct 2, 2020 at 8:37 PM Carlos Simmerling <
> > > > carlos.simmerling.gmail.com> wrote:
> > > >
> > > > > cpptraj will allow you to specify a different prmtop and
> > > > > reference coordinate set when doing RMSD calculations... it can get
> > > > > complicated if atoms don't match up, but your case sounds like a
> > single
> > > > > atom mask will give the same selection for both systems so it
> should
> > > work
> > > > > smoothly. Dan Roe or others might have more detailed advice, but
> this
> > > > works
> > > > > for me.
> > > > >
> > > > > I use something like this in my cpptraj script.
> > > > > load both prmtops, with a label for the alternate one
> > > > >
> > > > > parm ./prmtop
> > > > > parm ../build_40/prmtop [refparm]
> > > > >
> > > > > define reference structures, indicating the alternate prmtop for
> the
> > > > other
> > > > > system, and label each reference structure for use later:
> > > > >
> > > > > reference ./1min.rst7 [refinit]
> > > > > reference ../build_40/struct40.rst7 parm [refparm] ref [ref40]
> > > > >
> > > > > trajin ./md.x
> > > > >
> > > > > calculate rmsd to the SAME system:
> > > > >
> > > > > rmsd rms1 :10-70.CA,N,C,O out rmsd.10-70.dat ref [refinit]
> > > > >
> > > > > and then when doing the rmsd to the alternate system:
> > > > >
> > > > > rmsd rms2 :10-70.CA,N,C,O out rmsd.10-70.ref40.dat ref [ref40]
> > > > >
> > > > > On Fri, Oct 2, 2020 at 10:56 AM Vaibhav Dixit <
> > vaibhavadixit.gmail.com
> > > >
> > > > > wrote:
> > > > >
> > > > > > Dear Amber developers and users,
> > > > > > I have two structures identical except for a difference in
> > co-factor
> > > > > > charge.
> > > > > > Thus one has a Cl- ion extra added by tleap, but the number of
> > > > > > protein, non-standard residue and water atoms are identical.
> > > > > > Now, how do I compare the rmsd of the two trajectories snapshot
> by
> > > > > > snapshot?
> > > > > > Both trajectories start from the same PDB, thus I want to check
> if
> > > (how
> > > > > > much) there is a divergence in the coordinate-space that they
> > sample
> > > as
> > > > > > they move along the MD trajectories.
> > > > > > Is it possible/meaningful to compare reorganization of waters and
> > AA
> > > > > > between the two trajectories w.r.t. to coordinates and energies?
> > As
> > > > > > suggested earlier I will try to use imin=5 for this, but first I
> > > think
> > > > I
> > > > > > need to resolve incompatibility due to the extra Cl- ion. Both
> Cl-s
> > > > are >
> > > > > > 10 A from cofactor, so is it safe to simply ignore them and
> delete
> > > from
> > > > > > both prmtop before rmds or other analysis?
> > > > > >
> > > > > > I tried to use cpptraj to estimate rmsd for one trajectory using
> > > prmtop
> > > > > of
> > > > > > another which failed (then realized the small but important
> > > difference
> > > > > > between the two).
> > > > > > Is it possible to simply delete the extra/both Cl- from prmtop
> with
> > > > > parmed
> > > > > > and will it then work with cpptraj for all kinds of analysis.
> > > > > > Please suggest.
> > > > > > Looking forward to valuable suggestions from the list on this.
> > > > > > thank you and best regards.
> > > > > >
> > > > > >
> > > > > > --
> > > > > >
> > > > > > Regards,
> > > > > >
> > > > > > Dr. Vaibhav A. Dixit,
> > > > > >
> > > > > > Visiting Scientist at the Manchester Institute of Biotechnology
> > > (MIB),
> > > > > The
> > > > > > University of Manchester, 131 Princess Street, Manchester M1 7DN,
> > UK.
> > > > > > AND
> > > > > > Assistant Professor,
> > > > > > Department of Pharmacy,
> > > > > > ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
> > > > > > Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
> > > > > > VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
> > > > > > India.
> > > > > > Phone No. +91 1596 255652, Mob. No. +91-7709129400,
> > > > > > Email: vaibhav.dixit.pilani.bits-pilani.ac.in,
> > > vaibhavadixit.gmail.com
> > > > > > http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
> > > > > > https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
> > > > > >
> > > > > > ORCID ID: https://orcid.org/0000-0003-4015-2941
> > > > > >
> > > > > >
> > http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
> > > > > >
> > > > > > P Please consider the environment before printing this e-mail
> > > > > > _______________________________________________
> > > > > > AMBER mailing list
> > > > > > AMBER.ambermd.org
> > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >
> > > > > _______________________________________________
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> > > > >
> > > >
> > > >
> > > > --
> > > >
> > > > Regards,
> > > >
> > > > Dr. Vaibhav A. Dixit,
> > > >
> > > > Visiting Scientist at the Manchester Institute of Biotechnology
> (MIB),
> > > The
> > > > University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
> > > > AND
> > > > Assistant Professor,
> > > > Department of Pharmacy,
> > > > ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
> > > > Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
> > > > VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
> > > > India.
> > > > Phone No. +91 1596 255652, Mob. No. +91-7709129400,
> > > > Email: vaibhav.dixit.pilani.bits-pilani.ac.in,
> vaibhavadixit.gmail.com
> > > > http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
> > > > https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
> > > >
> > > > ORCID ID: https://orcid.org/0000-0003-4015-2941
> > > >
> > > > http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
> > > >
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Received on Sat Oct 03 2020 - 06:30:03 PDT
