[gmx-users] Combining two pdb

RAHUL SURESH drrahulsuresh at gmail.com
Wed Aug 15 14:15:54 CEST 2018

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?

*Rahul *

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