[gmx-users] Merge pdb files into single box
Javier Luque Di Salvo
jluquedisalvo at gmail.com
Thu Sep 20 18:27:15 CEST 2018
Then playing with cat, box dimensions and editconf + translations +
renumbering atoms/residues if needed should work.
> 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.
> > The pdb structures I would like to merge are very different from each
> > 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
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