Dear AMBER users,
I am trying to perform MM-PBSA calculations on a protein
ligand complex to estimate the ligands binding free energy.
I had some troubles in reproducing measured binding
constants and so I am checking what could have gone wrong.
Could you comment on the input file below? I think it
should generate trajectories that are suited to generate
coordinate snapshots for MM-PBSA calculations. I plan to
extract 100 snapshots after 10 ps each. My complex was
equilibrated for 25ps before.
I am a beginner in the field of molecular dynamics, so I am
not sure if I overlooked some significant parameter or set
all variables to reasonable values.
Thank you in advance for any comments.
Kind regards,
Thomas Steinbrecher
My AMBER7 input file for sander:
----------
cons pressure second production with T300K
&cntrl
imin = 0, nmropt = 0, ntx = 1, irest = 0,
ntrx = 1, ntxo = 1, ntpr = 5000, ntave = 0,
ntwr = 5000, iwrap = 0,
ntwx = 5000, ntwv = 0, ntwe = 0, ioutfm = 0,
ntwprt = 0, idecomp = 0,
ntf = 2, ntb = 2, dielc = 1, cut = 12.0,
scnb = 2.0, scee = 1.2, nsnb = 10, ipol = 0,
ibelly = 0, ntr = 0,
nstlim = 500000, nscm = 0, t = 0.0, dt = 0.002,
temp0 = 300.0, tempi = 300, ig = 71277,
heat = 0.0, ntt = 1, vrand = 0, tautp = 1,
vlimit = 20.0,
ntc = 2, tol = 0.00001,
ntp = 1, pres0 = 1.0, comp = 44.6, taup = 1,
&end
----------
Received on Sat May 24 2003 - 13:53:02 PDT
