Re: Membrane Protein Simulation Problems

From: Ilya Chorny (ichorny_at_gmail.com)
Date: Sat Oct 13 2007 - 11:57:56 CDT

What is a patch? I don't have any patches when running psfgen.

Thanks,

Ilya

On 10/13/07, Marcos Sotomayor <sotomayo_at_ks.uiuc.edu> wrote:
>
>
> (1) Have a look at
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/4566.html
>
> As with respect to CMAP or not CMAP, your log file indicates that you are
> using CMAP (1047 CROSSTERMS), so you are fine with that. Sorry about the
> confusion (and BTW, its not so good to send big files to everyone on the
> list).
>
> As with respect to CHARMM27, the charm27 files included in c31 should
> include CMAP (but those of previous versions do not, that's why I said
> that CHARMM27 does not include CMAP, sorry if that caused panic and
> confusion).
>
> I run out of options about how to diagnose what is happening with your
> simulation.
>
> Marcos
>
> On Sat, 13 Oct 2007, Ilya Chorny 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.

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