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

[Dawid das]

Hi,

I thought so because of what you said about PDB file. Yes, I will be of
course able to do it with Python.

Best wishes,
Dawid

2017-11-08 12:04 GMT+01:00 João Henriques <joao.m.a.henriques at gmail.com>:

> 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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