[gmx-users] g_lie + running MDS for a ligand only

vivek sharma viveksharma.iitb at gmail.com
Wed Oct 15 08:38:34 CEST 2008

Hi All,

I want to use g_lie function of gromacs to calculate the binding free energy
og a ligand with the protein. For the same I need to run two MDS, one for
ligand only and one for ligand+protein complex (please correct if I am
What are the checks that I should take care in this case, e.g. Do I need to
keep the same box size, or same number of solvation molecule in two cases ?
or similar things.

And also I am unable to run the MDS for ligand only as it gives the error
...Residue 'D4N' not found in residue topology database.....

For the ligand+protein complex I followed the drug-enzyme tutorial by J E
Kerrigan, and it worked well.
How can I run the MDS for ligand only ?................................ If I
will take the .itp from the PRODRG and use it as .top and bypass the pdb2gmx
step as mentioned in the tutorial, will it work ? (consider the difference
in two cases one is ligand only and other is ligand+protein ).

Please suggest...

With Thanks,
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