ADL: generate pdbqt from pdb with metal

Paul Rigor (uci) paul.rigor at uci.edu
Wed Mar 10 19:37:18 PST 2010


Hi gang,

In fact, most of the converted compounds have bonds marked as REMARKed...

Is there something I'm missing?  I'm using mgltools version 1.5.4

Thanks,
Paul

On Wed, Mar 10, 2010 at 7:31 PM, Paul Rigor (uci) <paul.rigor at uci.edu>wrote:

> Hi,
>
> I'm still having problems generating pdbqt from a pdb file.  I've included
> a sample compound from the Maybridge fragment library both the pdb
> (converted from sdf using babel) and the pdbqt generated by the ATD script.
>
> As you can see, the conversion is failing...
>
> Thanks,
> Paul
>
>
> On Tue, Mar 9, 2010 at 6:53 PM, Paul Rigor (uci) <paul.rigor at uci.edu>wrote:
>
>> Thank you, I'll try these out!
>>
>>
>> On Mon, Mar 8, 2010 at 8:20 PM, Stefano Forli <forli at scripps.edu> wrote:
>>
>>> Hi Paul,
>>>
>>> prepare_ligand4.py has two options that could suit your case:
>>>
>>>  [-g]    attach all nonbonded fragments
>>>        (default is not to do this)
>>>
>>>  [-p]    preserve input charges on atom type, eg -p Zn
>>>        (default is not to preserve charges on any specific atom type)
>>>
>>> Results may vary depending on your ligand geometry. The latter one is
>>> useful for keeping partial charges calculated with semi-empirical/QM methods
>>> (that's strongly encouraged).
>>>
>>> Hope this helps,
>>>
>>> Stefano
>>>
>>>
>>>
>>> Paul Rigor (uci) wrote:
>>>
>>>> Hi,
>>>>
>>>> I'm trying to prepare a ligand using the distributed prepare_ligand4.py
>>>> script.  The pdb structure however contains an iron metal.   Why is
>>>> everything but the metal getting erased? Basically, a ring structure
>>>> with a
>>>> coordinated Fe is rendered as just the Fe.
>>>>
>>>> What's the best way to prepare a ligand coordinated with a metal?
>>>>
>>>> Thanks,
>>>> Paul
>>>> ________________________________________________
>>>> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list---
>>>>
>>>
>>>
>>> --
>>>  Stefano Forli, PhD
>>>
>>>  Research Associate
>>>  Olson Molecular Graphics Laboratory
>>>  Dept. Molecular Biology,  MB-5
>>>  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/
>>>
>>
>>
>>
>> --
>> Paul Rigor
>> Pre-doctoral BIT Fellow and Graduate Student
>> Institute for Genomics and Bioinformatics
>> Donald Bren School of Information and Computer Sciences
>> University of California, Irvine
>> http://www.ics.uci.edu/~prigor
>>
>
>
>
> --
> Paul Rigor
> Pre-doctoral BIT Fellow and Graduate Student
> Institute for Genomics and Bioinformatics
> Donald Bren School of Information and Computer Sciences
> University of California, Irvine
> http://www.ics.uci.edu/~prigor
>



-- 
Paul Rigor
Pre-doctoral BIT Fellow and Graduate Student
Institute for Genomics and Bioinformatics
Donald Bren School of Information and Computer Sciences
University of California, Irvine
http://www.ics.uci.edu/~prigor


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