Re: [Apbs-users] convert .DX to UHBD format

[Nathan B. <ba...@bi...>]

Hi Davide --

> I have successfully downloaded and installed the distributed version of
> APBS and now I have access to use the tools (included dx2uhbd for the
> conversion of the grids).
>
> However, trying to convert the .dx files that I have in .grd format I get
> the following error:
> *
> Reading DX file ...
>   97 x 129 x 161 grid
>   (0.553679, 0.497542, 0.528469) A spacings
>   (39.2949, -3.6302, -36.757) A lower corner
> Writting UHBD file ...
> Vgrid_writeUHBD: can't write UHBD mesh with non-uniform spacing*
>
> This probably because I didn't compute the potential using a uniform
> spacing grids in the APBS calculation. Please, can you explain to me how I
> can compute a potential using a uniform spacing?
>

You are correct:  the UHBD format only supports uniform grid spacing.  If
you are performing an "mg-auto" calculation you can achieve uniform grid
spacing by setting all of the lengths in "fglen" and in "cglen" to be equal
and also setting all of the dimensions in "dime" to be equal.

Thanks,

Nathan

The .in file that pdb2pqr gives me doesn't calculate a uniform spacing grid.
> Please, can you tell me which parameters of the .in file from pdb2pqr I have
> to add/remove/change to have a proper calculation to subsequently transfor
> the grid in uhbd format?
>
> Thanks infintely for your help.
>
> Cheers,
> Davide
>
> 2009/8/31 Nathan Baker <ba...@bi...>
>
> Hello --
>> Are you using the version of APBS distributed with Ubuntu or did you
>> install it yourself?  I believe Ubuntu only ships with a limited version of
>> APBS; I would strongly recommend installing a recent version of APBS
>> available from http://apbs.sf.net/ so that you have access to all the
>> tools.
>>
>> -- Nathan
>>
>> On Aug 29, 2009, at 10:04 PM, Davide Mercadante wrote:
>>
>> Hi,
>>
>> thanks for the reply. I am using Ubuntu 9.04 debian platform. On my
>> machine the apbs folder seems to be in /usr/share/doc/apbs
>>
>> in this folder there isn't the folder share and neither the folder tools.
>> There is only the folder html that contains the user guide and the tutorials
>> (included the examples). Where I can find it?
>>
>> Thanks,
>> Davide
>>
>> 2009/8/30 Nathan Baker <ba...@bi...>
>>
>>> Hello --
>>> It should be available with APBS, often in a apbs/share/tools directory.
>>>  What OS are you using?
>>>
>>> -- Nathan
>>>
>>> On Aug 29, 2009, at 7:10 PM, Davide Mercadante wrote:
>>>
>>> Thanks!
>>>
>>> Sorry, how I can get this tool? Is not distributed with the APBS package?
>>> How I can get it?
>>>
>>> Thank you for any helps.
>>>
>>> Cheers,
>>> Davide
>>>
>>> 2009/8/30 Nathan Baker <ba...@bi...>
>>>
>>>> Hello --
>>>>
>>>> Yes, this is possible.  Please see the unsupported tool
>>>> tools/mesh/dx2uhbd
>>>>
>>>> Thanks,
>>>>
>>>> Nathan
>>>>
>>>>
>>>> On Aug 28, 2009, at 8:22 PM, Davide Mercadante wrote:
>>>>
>>>>  Dear APBS users,
>>>>>
>>>>> there is any way to convert the .dx output that comes out from APBS
>>>>> calculation in a UHBD format?
>>>>>
>>>>> Thanks,
>>>>> Davide
>>>>>
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>>>> Associate Professor, Dept. of Biochemistry and Molecular Biophysics
>>>> Director, Computational and Molecular Biophysics Graduate Program
>>>> Center for Computational Biology, Washington University in St. Louis
>>>> Web: http://bakergroup.wustl.edu/
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>>>
>>>  —
>>> Associate Professor, Dept. of Biochemistry and Molecular Biophysics
>>> Director, Computational and Molecular Biophysics Graduate Program
>>> Center for Computational Biology, Washington University in St. Louis
>>> Web: http://bakergroup.wustl.edu/
>>>
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>>  —
>> Associate Professor, Dept. of Biochemistry and Molecular Biophysics
>> Director, Computational and Molecular Biophysics Graduate Program
>> Center for Computational Biology, Washington University in St. Louis
>> Web: http://bakergroup.wustl.edu/
>>
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-- 
Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Director, Computational and Molecular Biophysics Graduate Program
Center for Computational Biology, Washington University in St. Louis
Web: http://bakergroup.wustl.edu/