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
>
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Received on Fri Oct 08 2010 - 11:00:05 PDT
