[gmx-users] Merge pdb files into single box

[Javier Luque Di Salvo]

Thanks Justin,

Then playing with cat, box dimensions and editconf + translations +
renumbering atoms/residues if needed should work.

Best regards

>
> On 9/20/18 10:28 AM, Javier Luque Di Salvo wrote:
> > Dear users,
> >
> > Browsing in the past threads I found that previous versions had the 'cat'
> > tool to merge two (or more) pdb structure files. I was wondering if this
> > tool is still available in current versions? I am using version 5.0.7
>
> cat is a Linux command, not a GROMACS program.
>
> -Justin
>
> > The pdb structures I would like to merge are very different from each
> other
> > and not-bonded among them, all I need is to put them inside the same
> > simulation box with no overlapping. Since the systems are quite big, I
> > would like to avoid manual manipulation with a molecular editor. A few
> > tests with trjcat gave me error because the systems are of different
> > composition, maybe I need to use trjcat with further options?
> >
> > Best regards
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================