[gmx-users] Writing pdb snapshot with charge from gro trajectory

[João Henriques]

Hi,

The PDB format is strict by definition (
http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html).
Every single character (and column) within a line has a specific purpose
and charges are not included there. I doubt trjconv or other gromacs tools
will allow you to tamper with it in such way. You can however make a simple
script to (i) parse the topology, (ii) match it with the PDB file, and
(iii) add an extra column at the end of the PDB with the respective
charges. This should be relatively simple to do with your favorite
scripting language.

Cheers,
J

On Wed, Nov 8, 2017 at 11:12 AM, Dawid das <addiw7 at googlemail.com> wrote:

> Dear Gromacs Users,
>
> I have a trajectory of my MD simulation in *.gro format. Is it possible to
> write the pdb snapshot
> from the trajectory so that the pdb file contains the atomic charge from
> top file?
> The charge should be put at the end of my pdb file.
>
> Best wishes,
> Dawid Grabarek
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