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"
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
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Received on Thu Oct 07 2010 - 23:00:05 PDT
