you can use ptraj to do this. lots of ptraj examples are in the Amber
tutorials,
the specific syntax for the dihedral command is page 251 of the Amber 9
manual.
your script might look something like:
#!/bin/csh
ptraj prmtop << EOF
trajin md.x
dihedral phi2 :1.C :2.N :2.CA :2.C out PHI2.data
go
EOF
On 8/31/07, Seth Lilavivat <sethl.gatech.edu> wrote:
>
> Dear Amber Users,
>
> How would I go about measuring a bond angle (the Glycosidic Bond) over
> the course of an MD simulation?
>
> Thanks,
> Seth
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Received on Sun Sep 02 2007 - 06:07:35 PDT
