Re: Membrane Protein Simulation Problems

From: Ilya Chorny (ichorny_at_gmail.com)
Date: Sat Oct 13 2007 - 11:26:57 CDT

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.

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