Re: NAMD-l: Get the PDB file from Steered Molecular Dynamics output files

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Fri Jun 17 2011 - 13:14:11 CDT

I assume you're referring to the NAMD binary coordinate file (.coor) that
is used for restart and final output. VMD can read those files and write
PDB files, but you'll need to read either input PSF and/or PDB file first
to fill in all of the atom names since .coor files are only coordinates.

You can also use the psfgen binary that ships with NAMD 2.8 thus:

you_at_host>/path/to/psfgen << END
? readmol pdb apoa1.pdb namdbin apoa1-out.coor
? writemol pdb apoa1-out.pdb
? END
PSFGEN 1.5.0 from NAMD 2.8 for Linux-x86_64
Info: reading file apoa1.pdb using plugin pdb
Info: reading coordinates from file apoa1-out.coor using plugin namdbin
WARNING: Plugin-based I/O is still in development and may still have bugs
Data fields found by plugin:
   Atomic number
   Occupancy
   B-factor
bonds: 0
Info: writing file apoa1-out.pdb using plugin pdb
WARNING: Plugin-based I/O is still in development and may still have bugs
total of 92224 atoms
total of 0 bonds
total of 0 angles
total of 0 dihedrals
total of 0 impropers
WARNING: Plugin-based I/O is still in development and may still have bugs
Info: file complete.

Note that you must put both files in the same readmol command.

-Jim

On Wed, 15 Jun 2011, albus hawking wrote:

> Dear all, I have used Steered MD to get the unfolding protein ubiquitin.
> And It works. Now I need to use the unfolding ubiquitin. So I would like
> to get the unfolding protein in PBC file. Could you please help me how
> to get the unfolding one from those output files of Steered MD? Thank
> you very much!
>

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