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
> >
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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 - 09:00:03 PDT
