Re: [AMBER] Perturbing residue co-ordinates within a solvated truncated octohedral box

From: David Case <>
Date: Sun, 7 Jul 2019 11:34:41 +0000

On Fri, Jul 05, 2019, Jack Shepherd wrote:

>1. Does anyone know of a suitable file type, that I could convert to and
>from rst or similar, which has the "long-form" information (particularly
>residue #) which would then be amenable to a bit of interference from a

The most straightforward thing to me seems to be to read in an .rst file
and the associated PDB template file (can be made once: you won't care
what the coordinates in it are); then output a modified .rst file.
Generate the PDB file using ambpdb on your starting coordinates.

You could also parse the prmtop file for this information (that is, in
fact, what ambpdb does).

This might be a case where setting ntxo to give an ASCII restart file
(rather than the default netcdf) would be warranted. Depends on how
often you need to do this, and how much time you have to spend writing
the script. If you're ambitious, learn how ParmEd reads and writes prmtop and
restart files.

...good luck....dac

AMBER mailing list
Received on Sun Jul 07 2019 - 05:00:02 PDT
Custom Search