[gmx-users] pdb generator

[Ali Ahmed]

well if you use Linux then you can use GVim to do highlight and do simple
changes on one type only then use find and replace option. That what I do
when I have more than one type. It needs one hour practice then you will be
ok. Or you can write a script for such things.
Best

On Tue, Nov 13, 2018 at 9:15 AM Momin Ahmad <momin.ahmad at kit.edu> wrote:

> Hi Ali,
>
> my problem is that there is not only one molecule but two different
> molecules which build up a crystaline structure. For example i have 10
> XXX and 100 YYY in the .pdb file.
>
> Cheers
>
> Momin
>
> Am 13.11.18 um 16:12 schrieb Ali Ahmed:
> > Hi,
> > I use Avogadro and it is easy to change LIG to anything you want. I just
> > use find and replace option which takes less than a minute.
> > Best
> > Ali
> >
> > On Tue, Nov 13, 2018 at 8:04 AM Momin Ahmad <momin.ahmad at kit.edu> wrote:
> >
> >> Hi,
> >>
> >> is there a tool where i can use for example a .cif file (or .xyz) file
> >> to generate a .pdb file with correct classification? For example
> >> Avogadro classifies all atoms as LIG and i cannot change it. Is there
> >> also another tool which can be used to generate large scale crystal
> >> structures with building blocks as input?
> >>
> >>
> >> Cheers
> >>
> >> Momin
> >>
> >> --
> >> Momin Ahmad
> >>
> >> Karlsruhe Institute of Technology (KIT)
> >> Steinbuch Centre for Computing (SCC)
> >> Hermann-von-Helmholtz-Platz 1
> >> 76344 Eggenstein-Leopoldshafen
> >> Phone: +49 721 608-24286
> >> E-Mail: Momin.Ahmad at kit.edu
> >>
> >> --
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> --
> Momin Ahmad
>
> Karlsruhe Institute of Technology (KIT)
> Steinbuch Centre for Computing (SCC)
> Hermann-von-Helmholtz-Platz 1
> 76344 Eggenstein-Leopoldshafen
> Phone: +49 721 608-24286
> E-Mail: Momin.Ahmad at kit.edu
>
> --
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