Re: [AMBER] Fwd: fixing rmsd values (follow-up)

From: Carlos Simmerling <carlos.simmerling.gmail.com>
Date: Tue, 27 Sep 2011 14:51:37 -0400

i'm not sure what's going on with your data, but (1) make sure you are up to
date with patches and (2) try the commands the way they are in my lab's
tutorial, which I know works for us. see below.

periodic imaging

*Here is a very important example for periodic imaging.* In this script, we
read a trajectory file from sander and image all of the atoms back to the
main box. This is important if you did not use iwrap=1 in your simulation.
Even if you do use iwrap=1, often the solute will diffuse to the edge of the
box and not appear to be fully surrounded by solvent. You want to put it
back in the middle of the box and then wrap the water back into the box.
This way when you look at the structures, they will always have the correct
water around their surfaces. This is needed for nice pictures, and for any
analysis of water around the solute.

It also is needed when you have more than one solute molecule (such as a
protein and ligand, or DNA duplex, or protein:DNA complex, or protein dimer,
and so on). The molecules can get separated when they are wrapped around the
periodic box (the basis of periodic calculations is too complex for this
tutorial, check a book such as the Leach Molecular Modeling book). If you
donít image the system properly, things like RMSD values will not be
correct. If you get huge RMSD values in a simulation with >1 solute
molecule, you probably need to image the trajectory file. Use VMD to see if
your molecules are getting separated, and if so, use ptraj to restore the
complex. (Note that this is not a real problem, just appears bad due to the
periodicity of the simulation).


 #!/bin/csh

This is for HIV protease, a dimer. We want to make sure the 2 monomers are
imaged properly, and not separated.


 ptraj parm.top << EOF
 trajin md6.mdcrd.gz
 trajin md7.mdcrd.gz

here we center the system on monomer 1, then wrap everything else back into
the main cell. This should restore our dimer.


 center :1-99 mass origin
 image origin center familiar

now we repeat the center/image commands, but for the dimer. This will put
the dimer in the box center and wrap the water around it.


 center :1-198 mass origin
 image origin center familiar

now we calculate the protein backbone RMSD as compared to the first snapshot
(we also could load a reference structure, but for this example it shows
using the first structure as the reference. This might be fine if the first
snapshot is the reference structure, which is probably the case if the
equilibration trajectory is included in the ptraj trajin command. It is also
fine if you only want to remove rotation and translation for viewing the
trajectory, but donít really care about the rmsd values. That is our goal
here, which is why we donít specify an output file for the rmsd.


 rms first :1-198.N,CA,C

now we save the imaged trajectory for later use, or viewing in VMD, etc.


 trajout md6-7.imaged.mdcrd
 EOF

------------------------------



On Tue, Sep 27, 2011 at 2:44 PM, Massimiliano Porrini <M.Porrini.ed.ac.uk>wrote:

> Dear Amber developers,
>
> I try to resend my email that probably was not read/received.
>
> Any hint to fix my RMSD values would be really appreciated.
>
> Cheers,
> M
>
>
> ---------- Messaggio inoltrato ----------
> Da: Massimiliano Porrini <M.Porrini.ed.ac.uk>
> Date: 26 settembre 2011 18:18
> Oggetto: Re: [AMBER] fixing rmsd values
> A: AMBER Mailing List <amber.ambermd.org>
>
>
> I really do not want to annoy you with this subject again,
> but even with the commands suggested by Bruno Rodrigues
> it did not work (it got actually worse, as you can see
> from the attached graph, I apologise about giving personal names
> to the solid lines, but it was the best way to make it clear).
>
> Besides now I am more confused than before about the right keywords to use
> to obtain a nice RMSD time series.
>
> I am very thankful for the hints though.
>
> All the best,
>
>
> Il 26 settembre 2011 16:54, Bruno Rodrigues <bbrodrigues.gmail.com> ha
> scritto:
> > Try this one:
> >
> > trajin tetra_dyn.dcd
> > center :1-11 mass
> > image origin center
> > center :1-22 mass
> > image center familiar
> > center :1-33 mass
> > image center familiar
> > center :1-44 mass
> > image center familiar
> > image familiar
> > reference tetra.pdb
> > rms reference mass out rmsd.dat .C,CA,N time 2
> >
> > On Mon, Sep 26, 2011 at 11:46 AM, Massimiliano Porrini
> > <M.Porrini.ed.ac.uk>wrote:
> >
> >> Dear Niel and dear all,
> >>
> >> Thanks very much for the hint, but, unless I am missing something here,
> >> unfortunately it did not work in my case.
> >>
> >> As I think my problem is exactly the same as the one presented in the
> post
> >> suggested by Niel, I updated my script commands:
> >>
> >> trajin tetra_dyn.dcd
> >> center :1-11 mass origin
> >> image origin center familiar
> >> center :1-22 mass origin
> >> image origin center familiar
> >> center :1-33 mass origin
> >> image origin center familiar
> >> center :1-44 mass origin
> >> image origin center familiar
> >> reference tetra.pdb
> >> rms reference mass out rmsd.dat .C,CA,N time 2
> >>
> >> And as you can see from the attached graph the RMSD has slightly
> >> improved, but still I get those jumps at the end.
> >>
> >> Any idea of what's happening here would be really appreciated.
> >>
> >> All the best,
> >>
> >>
> >> Il 25 settembre 2011 16:47, Niel Henriksen <niel.henriksen.utah.edu> ha
> >> scritto:
> >> > The Amber mailing list archive is a great resource to search:
> >> > http://archive.ambermd.org/
> >> >
> >> > It so happens that this issue has been discussed numerous times.
> >> > It is an imaging issue ... this post explains what to do nicely:
> >> > http://archive.ambermd.org/201103/0607.html
> >> >
> >> > If you search the archive there are lots of examples and a few
> >> > different approaches to dealing with it.
> >> >
> >> > Good luck,
> >> > --Niel
> >> > ________________________________________
> >> > From: Massimiliano Porrini [M.Porrini.ed.ac.uk]
> >> > Sent: Sunday, September 25, 2011 9:22 AM
> >> > To: AMBER Mailing List
> >> > Subject: [AMBER] fixing rmsd values
> >> >
> >> > Dear all,
> >> >
> >> > I have worked out the rmsd time series for a 30 ns trajectory
> >> > of my system, which is a tetramer of a 11-residues peptide
> >> > in explicit water, using the following ptraj commands:
> >> >
> >> > trajin tetra_dyn.dcd
> >> > center :1-44 mass origin
> >> > image :1-44 origin center
> >> > reference tetra.pdb
> >> > rms reference mass out rmsd.dat .C,CA,N time 2
> >> >
> >> > As you can see from the attached graph the rmsd time series bears
> >> > some "jumps".
> >> > These are due to the fact that the center of mass of one or more
> monomers
> >> > exceeds the boundaries of my cell (truncated octahedron) during the
> >> > simulation and
> >> > generate the high values of the RMSD.
> >> >
> >> > Does anybody know how I might fix the RMSD values via any ptraj
> commands?
> >> > Any suggestion would be really appreciated.
> >> >
> >> > Best,
> >> >
> >> > --
> >> > Dr Massimiliano Porrini
> >> > Institute for Condensed Matter and Complex Systems
> >> > School of Physics & Astronomy
> >> > The University of Edinburgh
> >> > James Clerk Maxwell Building
> >> > The King's Buildings
> >> > Mayfield Road
> >> > Edinburgh EH9 3JZ
> >> >
> >> > Tel +44-(0)131-650-5229
> >> >
> >> > E-mails : M.Porrini.ed.ac.uk
> >> > mozz76.gmail.com
> >> > maxp.iesl.forth.gr
> >> >
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >>
> >>
> >>
> >> --
> >> Dr Massimiliano Porrini
> >> Institute for Condensed Matter and Complex Systems
> >> School of Physics & Astronomy
> >> The University of Edinburgh
> >> James Clerk Maxwell Building
> >> The King's Buildings
> >> Mayfield Road
> >> Edinburgh EH9 3JZ
> >>
> >> Tel +44-(0)131-650-5229
> >>
> >> E-mails : M.Porrini.ed.ac.uk
> >> mozz76.gmail.com
> >> maxp.iesl.forth.gr
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >
> >
> > --
> > --
> > Bruno Barbosa Rodrigues
> > PhD Student - Physics Department
> > Universidade Federal de Minas Gerais - UFMG
> > Belo Horizonte - Brazil
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Dr Massimiliano Porrini
> Institute for Condensed Matter and Complex Systems
> School of Physics & Astronomy
> The University of Edinburgh
> James Clerk Maxwell Building
> The King's Buildings
> Mayfield Road
> Edinburgh EH9 3JZ
>
> Tel +44-(0)131-650-5229
>
> E-mails : M.Porrini.ed.ac.uk
> mozz76.gmail.com
> maxp.iesl.forth.gr
>
>
>
> --
> Dr Massimiliano Porrini
> Institute for Condensed Matter and Complex Systems
> School of Physics & Astronomy
> The University of Edinburgh
> James Clerk Maxwell Building
> The King's Buildings
> Mayfield Road
> Edinburgh EH9 3JZ
>
> Tel +44-(0)131-650-5229
>
> E-mails : M.Porrini.ed.ac.uk
> mozz76.gmail.com
> maxp.iesl.forth.gr
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Tue Sep 27 2011 - 12:00:05 PDT
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