[gmx-users] simulate a multimer with one component has covalently attached prosthetic group

[Debajyoti Dutta]

Hi all,

I am trying to simulate a dimer (say A2) where another protein is docked (say B) which is covalently attached with a prosthetic group. 

My question is how to do that. 

so far what i did ...

I generate a gro and itp file from PRODRG corresponding to that molecule and modified the charges based on the protocol mentioned in the paper 

http://pubs.acs.org/doi/abs/10.1021/ci100335w 

but, 

1) the atom which has to be linked with the protein B has taken a H which needed to be stripped; then how to generate the link with protein B.

2) The prosthetic group has a S atom in thioester form; I did not find a place that how and what charge to be assigned to that atom.

3) to to generate .rtp file for GROMOS 96 43a2 force field?

Thank you so much for your help

Debajyoti