AMBER Archive (2005)

Subject: AMBER: ptraj command inputs

From: opitz_at_che.udel.edu
Date: Wed Aug 10 2005 - 17:29:34 CDT


('binary' encoding is not supported, stored as-is) 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_at_2@N_at_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_at_C1@C2
:1_at_C3@C4_at_C5@C6_at_C7@C8_at_C9@C10_at_C11@C12_at_C13@C14_at_C15@C16_at_C17@C18_at_C19@C20_at_C21@C2
2_at_N1@N2_at_N3@N4_at_N5@N6_at_N7@N8_at_N9@N10 2-57
go

Thank you for any suggestions you might have.

Best Regards,

Armin

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