Re: [apbs-users] calculating the net dipole using APBS

[Barak B. <bar...@gm...>]

Hi,

I was just wondering if there's any progress with the PB dipole
calculation? Is it expected to be included in the next release of APBS?

Thanks,
Barak.


On Wed, Jul 31, 2013 at 11:00 AM, bbeng <bar...@gm...> wrote:

> Hi,
>
> Thank you for the quick reply.
> I would appreciate it a lot if the dipole information would be available
> on the next releases of APBS package (quadrupole is least significant).
> It is something that would be very useful for me :)
>
> Thanks again!
> Barak.
>
>
> On Tuesday, July 30, 2013 4:50:47 AM UTC+3, Baker, Nathan wrote:
>
>> Hi –
>>
>>
>>
>> We haven’t added that feature yet, partly because it is not obvious
>> whether the Coulombic or full Poisson-Boltzmann multipole moments would be
>> most useful.  The Coulombic multipole moments are easy to calculate but the
>> PB multipole moments would require more work.
>>
>>
>>
>> Thanks,
>>
>>
>>
>> ______________________________**____________________
>> *Nathan Baker*
>> Pacific Northwest National Laboratory
>> Tel:  +1-509-375-3997
>> http://nabaker.me
>>
>>
>>
>> *From:* bbeng [mailto:bara...@gmail.com]
>> *Sent:* Monday, July 29, 2013 6:41 AM
>> *To:* apbs-...@googlegroups.com
>>
>> *Cc:* Evelyne Deplazes; Libby, Steven; Stevens, Andrew J (PNNL); Baker,
>> Nathan
>> *Subject:* Re: [apbs-users] calculating the net dipole using APBS
>>
>>
>>
>> Hi,
>>
>>
>>
>> I've encountered this post when searching for a solution for getting the
>> dipole and quadruple moment of a protein.
>>
>> Have you already integrated this feature in the latest APBS version? If
>> not, how can I get this data?
>>
>>
>>
>> Thanks,
>>
>> Barak.
>>
>>
>> On Wednesday, February 13, 2013 6:06:41 AM UTC+2, Baker, Nathan wrote:
>>
>> Hello --
>>
>> We do not currently have an option for reporting the dipole moment of a
>> protein in APBS.  This information is actually calculated (thanks to Mike
>> Schnieders) when you run an APBS calculation with the "bcfl sdh" boundaries
>> conditions; however, we don't report the result to the user.  It would be
>> relatively straightforward to add print statements to the code (
>> http://sourceforge.net/p/**apbs/code/ci/**d8b8ef203030c0f4cfc8d98a58868f*
>> *38240a490c/tree/src/mg/vpmg.c#**l2662<http://sourceforge.net/p/apbs/code/ci/d8b8ef203030c0f4cfc8d98a58868f38240a490c/tree/src/mg/vpmg.c#l2662>)
>> to report the monopole, dipole, and quadrupole moments — if that would be
>> of general interest to the APBS community.
>>
>> Do you feel comfortable modifying the code yourself or would you like us
>> to do that?
>>
>> Thanks,
>>
>> --
>> Nathan Baker
>> Pacific Northwest National Laboratory
>> Phone: +1-509-375-3997
>> http://nabaker.me
>>
>> From: Evelyne Deplazes <evelyne....@hotmail.com<**mailto:
>> evelyne....@hotmail.com**>>
>> Date: Monday, February 11, 2013 3:26 PM
>> To: APBS-USERS mailing list <apbs-...@googlegroups.com<**mailto:
>> apbs-...@googlegroups.**com>>
>> Subject: [apbs-users] calculating the net dipole using APBS
>>
>> Hi APBS group (Hi Nathan)
>>
>> I have used APBS to calculate and then visualise the electrostatic
>> potential and electric field lines of a peptide (42 residues) and a ion
>> channel protein. My main interest is in looking at the interaction of the
>> peptide with the ion channel, in particular the orientation of the toxin
>> through the interaction with the electric field of the ion channel. For
>> that it would be good to calculate (and visualise) the net dipole of the
>> peptide. Is ther such an option in APBS?
>> Since the net dipole is "simply" a function of all the point charges in
>> the system which are probably calculated by APBS for visualising the
>> electrostatic surface potential I thought there might be an option to get
>> the vector for the net dipole of the molecule.
>> If this is not possible in the current code, any suggestions on how I
>> could calculate the vector for the net dipole of a molecule?
>>
>> thanks a lot
>> Evelyne
>>
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>>
>


-- 
Sincerely,
Barak