Porphyrin protonation state

HADDOCK
1

Dear all

I’m running Haddock for protein ligand interaction where the ligand is a porphyrin coordinating a Zn2+.

the calculation run finished successfully yet the PRODRG program protonates all the pyrroles within the porph ring. As suggested on the PRODRG server I added a string DELHYD N5 as follows

HETATM 127 H42 UNK 1 0.254 -11.977 -0.082 1.00 0.00 H
HETATM 128 H43 UNK 1 3.146 -8.757 0.084 1.00 0.00 H
HETATM 129 H44 UNK 1 4.936 -10.417 0.114 1.00 0.00 H
DELHYD N5
DELHYD N6
DELHYD N7
DELHYD N8
TER
HETATM 21 ZN+2 ZN2 2 -0.089 0.127 0.065 1.00 0.00 Z
TER
END

when I test the topology and parameterization of my porph running the prodrg server independently, the server does not add hydrogen on pyrroles, while when I run haddock on the web server keep on protonating the pyrroles.

Can you help me?

many thanks

Federica

2

The HADDOCK server is using a local (and older) version of PRODRG.
This simply won’t work.

If you want to have full control you will have to use a local version of the software and provide your own topology/parameter files.

3

clear. Thank you

on the online version of HADDOCK and the guru account is there a way to load my topol/param files?

best

4

No we don’t support upload of topo/param files as there might be too many things going wrong and this would affect the operation/throughput of the portal.
Sorry.

5

ok got it
thanks a lot