AMBER Archive (2008)

Subject: Re: AMBER: Res minimization

From: gurpreet singh (gps.iitm_at_gmail.com)
Date: Tue Jul 15 2008 - 23:25:54 CDT

HI THomas

Firstly as Ross pointed out you should look for any structural clashes in
the initial structure. Secondly you can also try using distance restraint
between the atoms of the ligand and protein.

Regards
Gurpreet

On 7/15/08, Thomas Leonard <thomasj_at_bii.a-star.edu.sg> wrote:
>
> 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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