[gmx-users] Merge pdb files into single box

Justin Lemkul jalemkul at vt.edu
Thu Sep 20 16:36:29 CEST 2018

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 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


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