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Dear Amber Community,
I'm trying to extract a radial distribution function from a trajectory
using ptraj in Amber7. I am having problems designating the two different
groups (solvent and solute in the manual, although neither group is
solvent here). The problem is that two atoms in residue 1 are group one,
but all the other atoms in residue 1 as well as other residues in the
molecule are in group 2. If I use the commands below ptraj only uses the
parts that pertain to residue 1, ignoring residues 2 through 57. Other
commands where I just add [.N10.2.N.C.O] to designate residue 2, atom
types O, N and C did not work.
Is there a way to designate atoms and residues in the ptraj input in Amber7?
trajin tmp.mdcrd 1 2 1
radial tmp 0.1 70 :1.C1.C2
:1.C3.C4.C5.C6.C7.C8.C9.C10.C11.C12.C13.C14.C15.C16.C17.C18.C19.C20.C21.C2
2.N1.N2.N3.N4.N5.N6.N7.N8.N9.N10 2-57
go
Thank you for any suggestions you might have.
Best Regards,
Armin
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Received on Wed Aug 10 2005 - 23:53:01 PDT
