[gmx-users] Generating coordinates for non-protein molecules

[deepa rajamani]

Hi,

I am trying to run MD simulations of protein with a small molecule system.

How can I include the coordinates of small molecules in the .gro file

How can I generate coordinates for the polar hydrogens which are not 
present in the small molecule pdb file.

I have used PRODRG to make the topology files for the small molecule.

I also tried approximating the coordinates of the small molecule and 
appending it to the protein.gro file. The only problem is that it does not 
have the polar hydrogens in it and the coordinates are approximated.

Thanks for any suggestions

Deepa