AMBER Archive (2007)

Subject: Re: AMBER: Measuring Bond Angle over simulation

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Aug 31 2007 - 14:34:13 CDT

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_at_C :2_at_N :2_at_CA :2_at_C out PHI2.data
go
EOF

On 8/31/07, Seth Lilavivat <sethl_at_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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