AMBER Archive (2007)

Subject: Re: AMBER: radius of gyration

From: priya priya (priyaanand_27_at_yahoo.co.in)
Date: Fri Jun 29 2007 - 08:14:49 CDT

yes radgyr command is working in amber9, i was just wondering why we need two input files for measuring radius of gyration.
Thanks!

Regards

Carlos Simmerling <carlos.simmerling_at_gmail.com> wrote: that is normal ptraj syntax. his example has two
input traj files. yours may have 1, or 7. The important
thing is the radgyr line. did you try it and get it to work?

On 6/29/07, priya priya <priyaanand_27_at_yahoo.co.in> wrote: hi in this command you have said to take two input files, may i know why.ptraj prmtop << EOF
trajin traj.1
trajin traj.2
radgyr out radgyr.dat :1-100
EOF

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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