Dear All :
Recently,I began to calculate the binding free energy by using the MMPBSA meathod.But when I prepared the .prmtop file I meet the problem.Following the MMPBSA tutorial , the script :
.........
NUMBER_LIG_GROUPS 1
LSTART 2622
LSTOP 3862
NUMBER_REC_GROUPS 1
RSTART 1
RSTOP 262
.............
In this script, I kown"RSTART 1 RSTOP 262" means the receptor is from atom 1 to 262. But consedering my system, there are two meatal ions, the protein is from residues 1 to 500, the ligand number is 501, then followned two ions(residues 502 and 503). I want to treat the protein and the meatal ions as the receptor, How could I deal with this if the number is not consecutive ? Thank you very much!
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Received on Mon Nov 08 2010 - 01:30:03 PST
