AMBER Archive (2008)

Subject: RE: AMBER: Res minimization

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Jul 15 2008 - 10:53:46 CDT

Hi Thomas,

Can you post your output file? Does the restraint energy increase a large
amount? A force constant of 500 should keep it very rigid although if you
have massive VDW clashes even that won't be able to hold it there. You could
try using ibelly to keep the ligand completely fixes, then it would need to
move the entire protein to one side to effectively move the ligand out of
the binding pocket.

I assume this is all in explicit solvent with periodic boundaries.

My suspicion is that you have some structural clashes in your starting
structure that are too severe for the minimization to correct for.

All the best
Ross

> -----Original Message-----
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> Of Thomas Leonard
> Sent: Tuesday, July 15, 2008 12:35 AM
> To: amber_at_scripps.edu
> Subject: AMBER: Res minimization
>
> Hi
>
> I am trying to minimize a ligand bound protein, in which the ligand always
> comes out of the binding pocket during the minimization.
>
> So tried res minimization. I wonder even in the res minimization the
> ligand comes out of the pocket even with a high force constant of 500.
>
> what is worng with my inputs
> please advice
>
> initial minimisation solvent + ions
> &cntrl
> imin=1, maxcyc=500,
> ntpr=5,
> ntr=1,
> &end
> Group input for restrained atoms
> 500.0
> RES 88 90
> END
> END
>
>
> Thomas
>
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