Re: Dock a metal ion into a peptide/protein

From: Branko (
Date: Wed Aug 31 2011 - 15:28:17 CDT


This is not a question for NAMD mailing list; anyway try with the GRID
(, there you have a Zn2+
probe, and you can estimate positions in your protein with high affinity
for it. Good way is to perform classical MD simulation of the protein
alone, than try with few snapshots from trajectory which have
significantly different conformations in the region where Zn ion could
bind well. Hope this will help

Kind regards


On 8/31/2011 9:29 PM, Andrea Holfelder wrote:
> Which is the best software to dock a metal ion into a protein .pdb
> file and generate a.pdb file of the "metalloprotein" ?
> While not exactly, but by some experiments,I know of a possible
> binding site in my protein and it has like pico molar affinity towards
> Zn+2 .
> Is there a good software to achieve this ?
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