[gmx-users] steric clash during docking experiment

Kai Zhuang kai.zhuang at gmail.com
Wed Jul 20 22:43:04 CEST 2005

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 :

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?

Kai Zhuang
BioMedical Engineering @ University of Toronto
kai dot zhuang at gmail dot com

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