Thank you for the advice. I used ambmask with the ":GLY.CA|.CB" mask and it
chose all the correct atoms. However, the output from ptraj is still:
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 there a known issue with ptraj's output of what atoms are masked? Is
there a good way within ptraj to see whether or not it is masking the
correct atoms besides the simple output?
Thanks again,
Tyler Glembo
On Fri, Oct 8, 2010 at 11:00 AM, Jason Swails <jason.swails.gmail.com>wrote:
> 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
> _______________________________________________
> 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
Received on Fri Oct 08 2010 - 12:30:03 PDT
