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,
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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
> > > >
> > > > 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
> >
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Received on Fri Oct 02 2020 - 14:30:02 PDT
