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,
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> > > 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
> > >
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> > >
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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
>
> P Please consider the environment before printing this e-mail
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Received on Fri Oct 02 2020 - 10:00:02 PDT
