[gmx-users] two pdb files

Justin A. Lemkul jalemkul at vt.edu
Wed Oct 15 14:04:09 CEST 2008

Vitaly Chaban wrote:
> Hi Justin,
> The only problem of you way is that numbers in the resulting '.gro'
> (after editconf -f *.pdb) file are wrong. But I still need it for the
> calculation, of course.

The resulting .pdb will have to be modified slightly, as Florian noted.  You can 
then renumber it with genconf -renumber to get continuous numbering.

If you need unique chain identifiers, that sort of thing could also be scripted 
if they are not already present.


> Do you know any software to succeed with this task?
> I tried to do it with MOLEKEL but (when I ask to save as PDB) it saves
> only the first structure (from the first PDB file).
> Thanks, Vitaly
> JAL> Vitaly Chaban wrote:
>>> Hi,
>>> I have two pdb files of two equal boxes (with different particles in
>>> them). I want just to concatenate them. I cannot do it with genbox
>>> because it inserts only a part of one box into another. But the boxes
>>> are absolutely equal. Thus, I need to insert box 'I' into box 'II'.
>>> The boxes are made in such a way that the molecules don't intersect
>>> after insertion.
>>> Does anybody know how to do it?
> JAL> cat pdb1.pdb pdb2.pdb > pdb_both.pdb
> JAL> -Justin
>>> Or the same with .gro files?
>>> Thanks.
>>> Vitaly


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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