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---- $ cpptraj >parm comdry.prmtop >trajin production_no_wat_ions_0_30.nc (complex of protein and ligand without water and ions) >rmsd ToFirst :671.C,N,O out ligand_0_30.rmsd time 0.002 >go ---- Calculation of delta delta G (as i understand) could be done with the values obtained from the final results obtained (from PB and GB caluculations). example: delta delta G = delta G1- delta G2 (separately for GB and PB) Please correct me if I am wrong. Also, do you feel that increasing the salt concentration has any effect in reducing the difference. ------- In response to Prof Luo's response.. Prasanth, I suggest that you look at the overall correlation and rmsd of relative affinities (delta delta G's) for all ligands instead of the agreement of the delta G of a single ligand. All the best, Ray -- Regards, Prasanth. _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Sun Apr 21 2019 - 23:30:02 PDT