AMBER Archive (2007)

Subject: Re: AMBER: radius of gyration

From: priya priya (priyaanand_27_at_yahoo.co.in)
Date: Mon Jun 25 2007 - 07:57:39 CDT

Hi
Thanks....this seems to work out now, i want to calculate radius of gyration only of the peptide excluding the water molecules,how can i specify that in the command line.

Regards
Thomas Cheatham III <tec3_at_utah.edu> wrote:
> i am using that command,but it says cannot read radgyr with mod (r).
> I have seen in the program,in ptraj, there is no file for radgyr.

OK, somehow ptraj is trying to read a file named "radgyr" and it cannot
find it or open it... This is unexpected unless you somehow did something
like "trajin radgyr".

Here is how I would run the radgyr command for a 100 residue protein:

ptraj prmtop << EOF
trajin traj.1
trajin traj.2
radgyr out radgyr.dat :1-100
EOF

-- tec3
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