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
Received on Fri Oct 08 2010 - 05:30:09 PDT
