[gmx-users] ions in PDB

Avell Diroll avelldiroll at yahoo.fr
Mon Mar 21 18:15:06 CET 2005


You don't have a chain name for your atom in this pdb file (between the 
second CA and 55).
I have got some pdb file with some Zn ions that are well recognised by 
In those pdb files the Zn ion is in the same chain as a protein ...
Hope that helped



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.

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