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---- Martin Lepsik, PhD student Phone: +420/2/20183-540, Fax: +420/2/20183-292 Dept. of Theor Chem & Center for Complex molecular Systems and Biomolecules Institute of Organic Chemistry and Biochemistry (IOCB) Flemingovo nam 2, Czech Academy of Sciences, 166 10, Prague 6, Czech Rep. URL: www.uochb.cas.cz/~teochem ----- Original Message ----- From: "Thomas Steinbrecher" <thomas.steinbrecher.physchem.uni-freiburg.de> To: <amber.heimdal.compchem.ucsf.edu> Sent: Saturday, May 24, 2003 2:36 PM Subject: MD input file for MM-PBSA calculations > 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 Mon May 26 2003 - 10:53:01 PDT