[gmx-users] Regarding numbering

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Jul 10 16:18:02 CEST 2009

Dear P.R.Anand Narayanan,

> 1. how did the number of atoms and residues change.

Hydrogen atoms were added to your structure, which accounts for the
increase in number of atoms. The number of residues should not have
changed. Probably there is a discrepancy between the number of
residues you have in your input file and the number of residues you
expect to have in it. Maybe there are two residues missing from the
list of coordinates?

> 2. while pasting the HETATMS of the cofactors and the related molecules
> necessary in the newly created pdb file (from that separate file), I changed
> the changed the number of atoms accordingly (that is numbers starting from
> 4454 to numbers starting from 5658). My question is that whether i should
> change the numbers of the residues also accordingly???? since the numbering
> of residues of cofactors and other necessary molecules werent in the
> sequentially ordered number.....

It's not necessary. From the MD point of view residue/atom numbering
is fully arbitrary, as long as your topology is consistent and matches
the atoms in the structure file.



Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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