AMBER Archive (2003)

Subject: Re: MD input file for MM-PBSA calculations

From: Lepsa (lepsik_at_marilyn.uochb.cas.cz)
Date: Mon May 26 2003 - 04:03:02 CDT

Thomas,
keep in mind that an MM-PBSA calculated on a trajectory of a protein-ligand
complex is an approximation that
dramatic conformational change in neither protein nor ligand occurs upon
binding (called rigid-binding approx - see Noskov, Biophys J, 2002). If this
is your case, you should calculate separate trajectories of protein, ligand
and complex.

Hope this helps,

Martin

P.S. Have you generated appropriate charges on ligand for PB calculations?
Also, betaP should be 0.92 (there is a mistake of 0.092 in some scripts)
----------------------------------------------------------------------------
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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_at_physchem.uni-freiburg.de>
To: <amber_at_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
> ----------