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 wrong). 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 like. ...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, Vivek
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