Try putting that mask into ambmask and see what atoms it says are selected.
That should tell you if it's doing what you expect.
Good luck!
Jason
On Fri, Oct 8, 2010 at 1:41 PM, Tyler Glembo <tglembo.asu.edu> wrote:
> I tried using that for a mask and the output from AMBER changes slightly
> to:
>
> Atom selection follows :1-19.CA
>
> ,:20-40,CA,:41-55,CA,:56-81,CA,:82-90,CA,:91-151,CA,:152-170,CA,:171-178,CA,:179-203,CA,:204-239,CA
> :240-249,CB
>
> Is it possible that the output from ptraj is wrong but AMBER is using the
> correct residues?
>
> Regards,
> Tyler Glembo
>
> On Fri, Oct 8, 2010 at 5:15 AM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
> > On Fri, Oct 8, 2010 at 1:50 AM, Tyler Glembo <tglembo.asu.edu> wrote:
> >
> > > Dear All,
> > > I am trying to do an rms between only C_betas for all residues except
> for
> > > GLY where I wish to choose C_alpha. My protein is 246 residues long
> and
> > > has
> > > 12 GLY at positions 19,39,40,55,etc. I tried both the following masks:
> > >
> > > ":GLY .CA | !:GLY .CB"
> > >
> >
> > Try this : ":GLY.CA | .CB" (note the lack of spaces). Since GLY
> doesn't
> > have a CB, this should do what you want.
> >
> > Good luck!
> > Jason
> >
> >
> > > and also
> > >
> > >
> > >
> >
> "(:ALA,ARG,ASN,ASP,CYS,GLN,GLU,HIS,ILE,LEU,LYS,MET,PRO,PHE,SER,TYR,THR,TRP,VAL
> > > .CB) & (:GLY .CA)"
> > >
> > >
> > > However, the output that I get from ptraj is as follows:
> > >
> > > Atom selection follows :1-19.CA
> > >
> > >
> >
> ,:20-40,CA,:41-55,CA,:56-59,CB,:61-81,CA,:82-90,CA,:91-151,CA,:152-170,CA,:171-178,CA,:179-197,CB
> > > :199-203,CA,:204-239,CA,:240-246,CB,:248,CB,:249.CB
> > >
> > > It seems that ptraj is choosing C_alphas at all times, except if there
> is
> > a
> > > GLY, then it decides to count a C_beta at the end, and for some reason
> it
> > > counts 18 C_betas between residues 179-197. Am I misreading the output
> > or
> > > perhaps not properly formating my mask string? Any help would be
> greatly
> > > appreciated.
> > >
> > > Regards,
> > > Tyler Glembo
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Fri Oct 08 2010 - 11:30:02 PDT
