ADL: Thnx for the advice...

Normandé Morrison normandemorrison at hotmail.com
Sat Nov 19 09:36:58 PST 2011


Thanks a lot for the advice... will run a new shoerte MD... it's gotta be it...

                                                                                                                                                                                                                                            
.Normandé Morrison. 



 > Date: Fri, 18 Nov 2011 14:33:27 -0800
> From: forli at scripps.edu
> To: autodock at scripps.edu
> Subject: Re: ADL: Could anyone help me please??
> 
> Hi Normandé,
> 
> I agree with Mihaly's hypothesis, especially if an MD is involved.
> Another thing thing that could help you to 'sanitize' a bit the input PDB could be to 
> pre-process the file with OpenBabel, with PDB as both input and output format. Sometimes 
> this helps to fix atom name misalignments and/or exotic naming conventions.
> 
> Hope this helps,
> 
> Stefano
> 
> On 11/18/2011 02:30 PM, Mihaly Mezei wrote:
> > Hi,
> >
> > your molecule probably was distroted at a few places, so some bonds appear to be broke and that confuses ADT. Try a short minimization of the final structure and see it ADT likes it better.
> >
> > Mihaly Mezei
> >
> > Department of Structural and Chemical Biology, Mount Sinai School of Medicine
> > Voice:  (212) 659-5475   Fax: (212) 849-2456
> > WWW (MSSM home): http://www.mountsinai.org/Find%20A%20Faculty/profile.do?id=0000072500001497192632
> > WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei
> > WWW (Department): http://atlas.physbio.mssm.edu
> > ________________________________________________
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> 
> -- 
>   Stefano Forli, PhD
> 
>   Research Associate
>   Olson Molecular Graphics Laboratory
>   Dept. Molecular Biology,  MB-112
>   The Scripps Research Institute
>   10550  North Torrey Pines Road
>   La Jolla,  CA 92037-1000,  USA.
> 
>      tel: (858) 784-2055
>      fax: (858) 784-2860
>      email: forli at scripps.edu
>      http://www.scripps.edu/~forli/
> ________________________________________________
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