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
> > > > >
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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 Sat Oct 03 2020 - 06:30:03 PDT
