[gmx-developers] How to name ions?

Alexey Shvetsov alexxyum at gmail.com
Wed Jul 28 17:48:37 CEST 2010

On Wednesday 28 of July 2010 19:05:31 Ran Friedman wrote:
> Hi,
> I'm in
favour of the second (simpler) option and (following the
> discussion)
suggest to have the same convention used in PDB files - atom
> and residue
names without the charge and in capital letters (e.g., ZN).
> This will also
eventually enable dealing with them using pdb2gmx (on
> most cases, see
> Problems:
> (1) Some atom names will be the same as in amino
acids, e.g., CD
> (cadmium) and CA (calcium). This is a minor issue in my
opinion but
> users should be aware of this because it may influence
> (2) How to deal with transition metals that have multiple
> states. For this I suggest to have the most common state as the
> and other state with different residue name, e.g., CU for Cu2+ and
> for Cu+. There are not too many cases like this for ions where FF
parameters are commonly available I guess. pdb2gmx may ask the user
explicitly how to deal with such ions.
> Thanks,
> Ran

Hi all!

think better to use namase such as Cu+ Na+ and so on as inernal ion naming
in forcefields with conversion from/to this naming scheme in pdb files (they
may have atom type names up to 4 characters long but its unusual. in most
cases 3 characters long names used in pdb)
Best Regards,
Alexey 'Alexxy'
Petersburg Nuclear Physics Institute, Russia
Department of
Molecular and Radiation Biophysics
Gentoo Team Ru
Gentoo Linux
mailto:alexxyum at gmail.com
mailto:alexxy at gentoo.org
mailto:alexxy at omrb.pn
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