AMBER Archive (2009)

Subject: [AMBER] PDB of a specific frame

From: Jason A. Ford-Green (jgreen_at_ccmsi.us)
Date: Wed Feb 04 2009 - 13:46:52 CST

 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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