[gmx-users] ions in PDB

Maik Goette mgoette at mpi-bpc.mpg.de
Tue Mar 22 14:42:11 CET 2005


Have a look at your forcefield. If Ca is included there, try to rename 
the PDB.
If not, you can do it manually, but you need the parameters for Ca then.
Remember the coordinates in PDB are A, in GRO are nm.


Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/

Alan Wilter Sousa da Silva wrote:
> Hi List!
> I have a PDB with a Calcium ion present. Using pdb2gmx I loose this ion.
> PDB line:
> HETATM 2447 CA    CA    55     -22.825  26.876  -2.752  1.00 20.89
> Should I have to change the calcium name in PDB file to a special name 
> that pdb2gmx is able to recognise, or GMX is not able to identify it.
> If not, how to insert a Ca+2 ion at the exact place from where the original 
> one was removed by pdb2gmx?
> Many thanks in advance for any help.
> Cheers!
> Alan

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