Hello all,
I am using PRODRG server for ligand topology file but in case of B12 as a ligand, contain different type of atom like Cobalt etc, when i submit the the input to the server it gives the error like this:
PRODRG> Starting up PRODRG version AA100323.0717 PRODRG> Parameter set 'pd/gromos96' (fftype=2). PRODRG> PDB mode detected. PRODRG> Found unsupported atom type CO (atom 'CO ') in your coordinates. ERRDRG> Currently only N, C, O, S, P, Cl, Br, F, I are supported. PRODRG> Program terminated unsuccessfully, sorry!
How can i make the coordinate file for this ligand?
You can not generate topology file from PRODRG server. Its the metal, this server don't deal with metal ions. For that you need to jump to QM calculations.
Hi,
Instead of PRODRG you can switch to ATB server and select "gromos53a6" forcefield. As far as I know this force field has the metals.
All the best.
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