Re: [Apbs-users] SDH in APBS 0.5.0

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

Hi All --

We've checked in a version (revision 1094) of APBS into Subversion  
which fixes this issue.  Our Subversion repository is publicly- 
accessible using the instructions at

	http://sourceforge.net/svn/?group_id=148472

We'll hurry to prepare an official release of APBS which incorporates  
this bug fix.

Thanks Scott for finding this!

-- Nathan

On May 27, 2007, at 9:47 AM, Bradley Scott Perrin wrote:

> Thank you for your help. I'll try 'bcfl mdh'.
>
> -Scott
>
> ----- Original Message -----
> From: Nathan Baker <ba...@cc...>
> Date: Saturday, May 26, 2007 8:59 pm
> Subject: Re: [Apbs-users] SDH in APBS 0.5.0
>
>> Hello --
>>
>> Yes, you're correct:  'bcfl sdh' appears to be behaving like 'bcfl
>>
>> zero'.  New boundary condition code was added into APBS in version
>>
>> 0.5.0.  This code doesn't affect 'bcfl mdh' or focusing.
>>
>> We'll take a look at this and see if we can fix it quickly.  In
>> the
>> meantime, I'd suggest using 'bcfl mdh'.
>>
>> Sorry for any inconvenience this might cause.
>>
>> -- Nathan
>>
>>
>> On May 25, 2007, at 5:32 PM, Bradley Scott Perrin wrote:
>>
>>> Nathan,
>>>
>>> Thank you for the reply. Attached are the pqr files.
>>>
>>> -Scott
>>>
>>>
>>> ----- Original Message -----
>>> From: Nathan Baker <ba...@cc...>
>>> Date: Friday, May 25, 2007 6:16 pm
>>> Subject: Re: [Apbs-users] SDH in APBS 0.5.0
>>>
>>>> Hello --
>>>>
>>>> That's strange.  Based on the changes made (added multipole
>>>> support)
>>>> for 'bcfl sdh' in version 0.5.0, it should behave *less* like 'bcfl
>>>>
>>>> zero'.  Can you send the PQR file so we can test this?
>>>>
>>>> Thanks,
>>>>
>>>> Nathan
>>>>
>>>> On May 25, 2007, at 2:20 PM, Bradley Scott Perrin wrote:
>>>>
>>>>> Hello APBS Users,
>>>>>
>>>>> In APBS 0.5.0, I received the same result using 'bcfl sdh' as
>>>> 'bcfl
>>>>> zero'. When performing the same calculation under APBS 0.4.0,
>>>> 'bcfl
>>>>> sdh' gave much better numbers than 'bcfl zero' (as expected).
>>>>>
>>>>> Any ideas on how I managed this?
>>>>>
>>>>> I've attached a sample input file. The size of the molecule is
>>>>> roughly 45 x 45 x 45 A^3.
>>>>>
>>>>> -Scott
>>>>> <test_sdh.in>
>>>>> ---------------------------------------------------------------
>> ---
>>>> ----
>>>>> ---
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>>>>
>>>> --
>>>> Associate Professor, Dept. of Biochemistry and Molecular Biophysics
>>>> Center for Computational Biology, Washington University in St.
>> Louis>> Web: http://cholla.wustl.edu/
>>>>
>>>>
>>>> <4fsr_ar.pqr>
>>>> <1hip_ar.pqr>
>>
>> --
>> Associate Professor, Dept. of Biochemistry and Molecular Biophysics
>> Center for Computational Biology, Washington University in St. Louis
>> Web: http://cholla.wustl.edu/
>>
>>

--
Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology, Washington University in St. Louis
Web: http://cholla.wustl.edu/