Re: Membrane Protein Simulation Problems

From: Ilya Chorny (ichorny_at_gmail.com)
Date: Sat Oct 13 2007 - 11:46:26 CDT

No it's ok. I think I might not have the CMAP cross terms. Please see my
previous posts. I am actually using C31, but within C31 I am using top_all27
which does not seem to have the CMAP crossterms. I am not even sure what
CMAP stands for. :) I will have to look it up. Maybe I should switch to
OPLS? That is the forcfield I am most comfortable with.

Thanks,

Ilya

On 10/13/07, L. Michel Espinoza-Fonseca <mef_at_ddt.biochem.umn.edu> wrote:
>
> You should be more than fine by using the CHARMM27 ff. Sorry for all
> this confusion!
>
> 2007/10/13, Ilya Chorny <ichorny_at_gmail.com>:
> > Ok, sorry to bombard everyone with emails but I just took a close look
> at
> > the topology files within C31b1 and it looks like the top_all22 has the
> cmap
> > and not the top_all27. Should I be using the top_all22? I am confused.
> >
> >
> > Thanks,
> >
> > Ilya
> >
> >
> > On 10/13/07, Ilya Chorny <ichorny_at_gmail.com> wrote:
> > > 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.
> > >
> >
> >
> >
> > --
> > Ilya Chorny Ph.D.
> >
>

-- 
Ilya Chorny Ph.D.

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