AMBER Archive (2009)

Subject: Re: [AMBER] PDB of a specific frame

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Feb 04 2009 - 13:52:49 CST

what do you get as output from ptraj?
usually you use a syntax like
trajin start end
and you will get a pdb file (if that's what you ask for) for each of
the frames in the range. you only gave 1 number after teh filename.
perhaps a single # works in the trajin, but i usually do:

trajin file 50 50

does your resulting pdb file have frame number appended to filename?
how do you know if it "matches" or not- what analysis is telling you
ptraj doesn't write the correct frame?

also, if you run the entire traj file against the ptrajout pdb file,
do any of the frames match? that might help you troubleshoot.

On Wed, Feb 4, 2009 at 2:46 PM, Jason A. Ford-Green <jgreen_at_ccmsi.us> wrote:
>
> All,
>
> I would like to know if there is a ptraj command for making a pdb file of a particular frame in a trajectory file. This trajectory is a specific temperature from an replica exchange MD calculation. I am interested in a particular frame. We have tried the following script, but when I do an RMSD of my frame of interest (from the temperature trajectory file) with the pdb structure (made from the ptraj script below) of same frame It doesn't match. Any help would be greatly welcome.
>
>
> #!/bin/bash
>
> ptraj jprotpol_h_REMD_64_GB_NoLig.prmtop <<EOF
> trajin remd.Ttraj_64_GB_NoLig.308.2.mdcrd 95
> trajout frame95_308.2K.pdb PDB
> go
> EOF
>
> done
>
>
> Thanks for your help and sorry about the extremely long filenames.
>
> Cheers,
>
> Jason Ford-Green
>
>
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