[gmx-users] Atom names mismatch - PyMol retain order

[Martin Höfling]

Am Freitag, 30. Mai 2008 schrieb George Abadir:

> atoms. Then in the simulation I used the initial PDB file generated by
> PYMOL. Does this make things any more reasonable. Because actually, this
> happened in five different simulations till now!!!! So, I don't think it

Just as a side comment on using PYMOL: If one wants to preserve ordering of 
atoms on loading and thus exporting one can set this (e.g. in the .pymolrc).

This is what I use for editing molecules generated with pdb2gmx.
...
set retain_order,1
set pdb_retain_ids,1
...

Best
	Martin