so I am able to load output crd with VMD and check dihedral angles for 4
atoms. But comparing the value calculated from VMD for the same frame does
not match the value extracted by ptraj.
the molecule I use is alpha-lactose, which is
beta-galactose-1-4-alpha-glucose
The four atoms to define phi are H1, C1 from galactose and O4 C4 from
glucose
the ptraj_in file is
*trajin md_output.crd 25 125 1
dihedral phi :2.H1 :2.C1 :3.O4 :3.C4 out aLac_phi.out
go*
Is this file correct? I got another version from tutorial is
*trajin md_output.crd 25 125 1
dihedral phi :2.H1 :3.C1 :3.O4 :3.C4 out aLac_phi.out
go*
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Received on Fri Mar 18 2011 - 14:00:03 PDT
