[gmx-users] steric clash during docking experiment

[David van der Spoel]

On Wed, 2005-07-20 at 16:43 -0400, Kai Zhuang wrote:
> Hi all,
> I'm trying to perform a docking experiment by manually dragging the
> ligand close to the binding pocket.  ideally i want the ligand to be
> half inside the pocket.  however, when i do this manually with VMD or
> DeepView, there's no warning if i made a steric clash or such.
> 
> when i run EM, i get :

better starting structure obviously, and maybe the l-bfgs algorithm can
help, and maybe double precision.


> 
> Polak-Ribiere Conjugate Gradients:
>    Tolerance (Fmax)   =  2.00000e+02
>    Number of steps    =         1000
>    F-max             =  1.71932e+17 on atom 12998
>    F-Norm            =  2.43149e+17
> 
> the system has way too much energy, and the run dies with in one interation:
> 
> Polak-Ribiere Conjugate Gradients converged to machine precision in 0 steps,
> but did not reach the requested Fmax < 200.
> Potential Energy  =  1.1445830e+13
> Maximum force     =  4.6792724e+15 on atom 12998
> Norm of force     =  2.1982580e+14
> 
> what should i do? is there anyway to avoid such clashing during the
> preparation stage (ie. a better software exists for this type of
> manual docking) or some way to keep EM running long enough to fix the
> problem itself?
> 
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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