[gmx-users] Generating coordinates for non-protein molecules
deepsri at bu.edu
Fri Aug 5 22:39:35 CEST 2005
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
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