Sample input file for MMPBSA with membrane proteinsThis input file is meant to show only that gmx_MMPBSA works. Althought,we tried to used the input files as recommended in the Amber manual,some parameters have been changed to perform more expensive calculationsin a reasonable amount of time. Feel free to change the parameters according to what is better for your system.&generalsys_name="Prot-Memb",startframe=1,endframe=4,/&pbmemopt=1, emem=7.0, indi=4.0,mctrdz=-10.383, mthick=36.086, poretype=1,radiopt=0, istrng=0.150, fillratio=1.25, inp=2,sasopt=0, solvopt=2, ipb=1, bcopt=10, nfocus=1, linit=1000,eneopt=1, cutfd=7.0, cutnb=99.0,maxarcdot=15000,npbverb=1,/
The thickness is controlled by the mthick option (36.086 Å in this case). The center of the membrane region is controlled with mctrdz and in this case the membrane region will be centered at -10.383 Å down of the center of the protein. If calculations are performed on a protein with a solvent-filled channel region, this region would be identified automatically by setting poretype=1.
