Re: Membrane Protein Simulation Problems

From: Ilya Chorny (ichorny_at_gmail.com)
Date: Sat Oct 13 2007 - 11:37:09 CDT

HI All,

For further clarification I am using C31B1 which is the charmm 31 forcefield
but with C31b1 I have the option to chose top/par 22 or top/par 27. I chose
top/par 27.

Thanks,

Ilya

On 10/13/07, Ilya Chorny <ichorny_at_gmail.com> wrote:
>
> Attached is a copy of my log file.
>
> Thanks,
>
> Ilya
>
>
> On 10/13/07, Ilya Chorny <ichorny_at_gmail.com > wrote:
> >
> > Marcos,
> >
> > Can you clarify (1) for me. What do you mean by applying patches?
> >
> > I do align my proteins when calculating the RMSD but even after the
> > alignment the RMSD looks like the diffusion equation Sqrt(6DT).
> >
> > Thanks,
> >
> > Ilya
> >
> >
> > Thanks
> >
> > On 10/13/07, Marcos Sotomayor < sotomayo_at_ks.uiuc.edu> wrote:
> > >
> > >
> > > Just to clear up the confusion (I might be wrong though)
> > >
> > > -The protein forcfield is the CHARM22 forcefield. It has
> > > not changed at all in the version 27 or 31 of CHARMM, except that in
> > > CHARMM31
> > > they provided the CMAP corrections, which you should apply on top of
> > > the
> > > CHARM22 force-field.
> > >
> > > -The difference between CHARM22 and CHARM27 is in the lipid
> > > parameters, which are not affected by CMAP.
> > >
> > > -So, just to be sure that you are using the parameter and topology
> > > files provided in the version 31 (or >31) of CHARMM (the software) and
> > > that your psf file does include the CMAP terms and that NAMD is
> > > actually
> > > using the CMAP correction: check CROSSTERMS in the log file (you
> > > should
> > > have more than 6 under STRUCTURE SUMMARY).
> > >
> > > I hope I did not confuse people even more....
> > >
> > > Two more comments for Ilya: (1) if you are applying patches during psf
> > >
> > > file generation (outside the generate statement), be sure to use the
> > > regenerate angle dihedrals command [This is important when using
> > > topology files from c31b1 and c32b1] (2) be sure to align your protein
> > > before computing RMSDs.
> > >
> > > Regards,
> > > Marcos
> > >
> > > On Sat, 13 Oct 2007, L. Michel Espinoza-Fonseca wrote:
> > >
> > > >>> My understanding from the previous email is that 27 has the CMAP
> > > corrections
> > > >>> as well.
> > > >>
> > > >> 22 and 27 do not include CMAP, which was released with 31. However,
> > > the
> > > >> labeling is quite confusing and I see that you seem to be using the
> > > right
> > > >> parameter file (which is labeled 27 and includes CMAP!?). Check the
> > > number
> > > >> of CROSSTERMS in your log file (STRUCTURE SUMMARY section) to be
> > > sure
> > > >> that you are using CMAP.
> > > >
> > > > Just a single comment:
> > > >
> > > > CHARMM 27 *does* include the CMAP correction. When using this
> > > version
> > > > of the ff, your NAMD log file shows that you have "x" number of
> > > > crossterms. I've been using the CHARMM 27 ff for the stability of
> > > > helices and you can indeed see the difference in terms of stability.
> > >
> > > > In fact, the paper by Buck et al. mentions such correction as
> > > > "C22/CMAP".
> > > >
> > > >>
> > > >>>
> > > >>> "reinitvels" must not be working because I do not assign a
> > > temperature, thus
> > > >>> it would not know what distribution to select from. I have since
> > > removed
> > > >>> this option. Not even sure how it got into my script.
> > > >>
> > > >> Indeed, you are not using the "temperature" command, but your
> > > posted
> > > >> configuration files has a "set temperature 310" command and
> > > >> a "reinitvels" command (the command does work and you were
> > > overriding
> > > >> velocities in that particular case; note the subtle difference
> > > between
> > > >> the TCL variable temperature and the NAMD command temperature).
> > > >>
> > > >>>
> > > >>> Temperature averages out to 310K. The PME grid is 128x128x128.
> > > >>
> > > >> What is the size of the simulation box?? Is there enough space
> > > between
> > > >> periodic images?
> > > >>
> > > >>> 1.4 A resolution.
> > > >>
> > > >> Is the whole protein or a particular zone getting deformed? you may
> > > >> want to compute RMSD for some zones of the protein or compute RMSD
> > > per
> > > >> residue and check what part of the protein is behaving badly. By
> > > the
> > > >> way, when you said that your RMSD was going up, how bad is it? 2,
> > > 3, 6 A?
> > > >> I would also suggest to look at protonation states carefully (as
> > > suggested
> > > >> by Richard).
> > > >>
> > > >>> Hope that helps,
> > > >>>> Marcos
> > > >>
> > > >>
> > > >
> > >
> >
> >
> >
> > --
> > Ilya Chorny Ph.D.
> >
>
>
>
> --
> Ilya Chorny Ph.D.
>
>

-- 
Ilya Chorny Ph.D.

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