[gmx-users] Fwd: Topology error

Jai Krishna krishnamjai at gmail.com
Mon May 22 12:55:15 CEST 2017

Dear Sir/Ma'am,

I am trying to generate topology file for my metalloprotein that has FeS
cluster and Fe2+ atoms in it. When I run the pdb2gmx command, it fails to
generate the topology file. The error says -   Residue 'FE2' not found in
residue topology database.

Could you please help me with this query? What steps should I take to
proceed forward with it. I also like to tell you that I need these atoms in
my protein for ligand to bind and for simulation also.

Thank you in advance.

Jai Krishna
IIT Roorkee

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