[gmx-users] Combining two pdb

Justin Lemkul jalemkul at vt.edu
Wed Aug 15 14:17:47 CEST 2018

On 8/15/18 8:11 AM, RAHUL SURESH wrote:
> Hi. I tried combining two pdb's such that, 1-24res of PDB X with 25-72 res
> of PDB Y. I used pymol to do this. I just aligned the protein in such a way
> that the N terminal of one protein is near the C terminal of the other. I
> haven't made any physical bonds between them and saved as pdb. I have
> equilibriated the structure for 500ps and found normal, but when visualixed
> in chimera or discovery studio, it shows a gap between the structure.
> Is there any fault in the methodology that I follow?
That depends on how you generated the topology. What you see in 
visualization software is not necessarily real. The only way to know if 
bonds are there or not is to look at the topology.



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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