[gmx-users] Issue with the PDB generated after topology

Mark Abraham mark.j.abraham at gmail.com
Mon Jul 3 13:35:56 CEST 2017


Sure, they're all just labels. If you wanted to look at the heights of the
girls in a family and the heights of boys in the same family, sorted by
age, then e.g. boy 2 could easily be child 5... You just need to think
about simulation residue number differently from input residue number.
Neither "should" be used - but each is convenient for a different purpose.


On Mon, Jul 3, 2017 at 1:31 PM Khadija Amine <kh.amine1 at gmail.com> wrote:

> Thank you, Mark.
> I understand from your suggestion, that what I got from topology and
> solvation phases is correct, and MD simulations even if it affects the
> numbering of the structure but the simulation results remain unaffected and
> I could renumber my residues at the end of simulation as it should be.
> This the first time I'm facing this case as it's the first time I'm running
> MD simulation of a protein complex.
> Khadija
> *Khadija Amine*
> Ph.D. Biology and Health
> Biochemistry & Bioinformatics
> Phone: 33339584
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