What happens when you load the wrapped trajectory, like in Carlos' script?
What does really happen with the solute. It can then give a good indication
about what is wrong. Does one or two strands go to the next cell? Or does
the system has any kind of sharp denaturation (probably not, but we never
know...)?
I've learned some stuff from my work with RMSD, and it sounds that a part
of your molecule really went to the next cell. And I tell you more, the
distance between 2 cells is around 20-25 angstroms, which means that you
have a 12 angstroms solvent layer around your solute. I would say that it's
too few for a 44 residues molecule. I use 12 angstroms for a 20 residues.
Maybe someone more experienced can tell something more.
On Tue, Sep 27, 2011 at 6:14 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> to follow up on Tom's last sentence ("make it so all the molecules are
> together in the prmtop"), here is a bit of info on how to do it:
>
> Modify the pointers in your prmtop so that all the solute molecules are in
> 1
> "molecule"
>
> - here is a sample prmtop for a dimer- the goal is to put both monomers
> into a single "molecule"
>
>
> %FLAG SOLVENT_POINTERS
> %FORMAT(3I8)
> 830 10924 3
>
>
> -
> - this data is really in this format
>
>
> FORMAT(12I6) IPTRES, NSPM, NSPSOL
> IPTRES : final residue that is considered part of the solute,
> reset in sander and gibbs
> NSPM : total number of molecules
> NSPSOL : the first solvent "molecule"
>
>
> -
> - what you need to do is to
> - leave IPTRES alone (your solute is not changing)
> - change NSPM to match your "new" # molecules (if you make a dimer
> into a single molecule, subtract 1. if you make 3 molecules
> into 1, subtract
> 2).
> - change NSPSOL the same way- subtract 1 or 2 or more, depending on
> what you subtracted from NSPM
> - here is the "new" SOLVENT_POINTERS section that turns the 2 monomers
> in a single molecule:
>
>
> %FLAG SOLVENT_POINTERS
> %FORMAT(3I8)
> 830 10923 2
>
>
> - now for the next section to change- atoms per molecule.
>
>
> %FLAG ATOMS_PER_MOLECULE
> %FORMAT(10I8)
> 6015 6015 3 3 3 3 3 3 3
> 3
> 3 3 3 3 3 3 3 3 3
> 3
>
>
> -
> - what you want to do is combine the first two "molecules" (the
> monomers) into a single molecule.
> - change the "atoms per molecule" to combine the atoms from the two
> molecules
> - in this case, 6015+6015=12030
> - move the numbers up- in this case, change the second 6015 to a 3,
> and delete the last 3 at the end of this section.
> - here is the modified section (not showing the removal of the final 3
> from the end of this section- bu make sure you delete it).
>
>
> %FLAG ATOMS_PER_MOLECULE
> %FORMAT(10I8)
> 12030 3 3 3 3 3 3 3 3
> 3
> 3 3 3 3 3 3 3 3 3
> 3
>
>
> - *SAVE THIS TO A NEW FILE NAME, MAKING IT CLEAR BY THE NAME THAT YOU
> MODIFIED THE MOLECULE POINTERS*
>
>
> On Tue, Sep 27, 2011 at 4:55 PM, Thomas Cheatham III <tec3.utah.edu>
> wrote:
>
> >
> > > I try to resend my email that probably was not read/received.
> > > Any hint to fix my RMSD values would be really appreciated.
> >
> > There is probably not an easy way to fix. Look through the archive as
> > suggested about imaging issues and try things like center only the first
> > residue of each chain, etc. and imaging. Imaging based on the first atom
> > rather than center of mas, etc.
> >
> > This was what prompted the question on the reflector back to you about
> box
> > size / amount of solvent. Likely there is too little, so there is not an
> > easy way to, by generic procedure, image the molecules back since the
> > periodic image may be closer than the unit cell, i.e. once it is wrapped,
> > it becomes closer to its image.
> >
> > I have been meaning to write a smarter imaging routine that would attempt
> > to minimize distances, however I have not done this.
> >
> > There are ways to make it so all the molecules are together in the prmtop
> > which will prevent this.
> >
> >
> > --tec3
> >
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--
--
Bruno Barbosa Rodrigues
PhD Student - Physics Department
Universidade Federal de Minas Gerais - UFMG
Belo Horizonte - Brazil
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Received on Tue Sep 27 2011 - 15:00:02 PDT
