Thread: Re: [apbs-users] calculating the net dipole using APBS
Biomolecular electrostatics software
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From: Baker, N. <Nat...@pn...> - 2013-02-13 04:06:52
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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/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 <eve...@ho...<mailto:eve...@ho...>> Date: Monday, February 11, 2013 3:26 PM To: APBS-USERS mailing list <apb...@go...<mailto:apb...@go...>> 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 |
From: Francois B. <ber...@ri...> - 2013-02-13 04:41:23
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On 02/13/2013 01:06 PM, 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/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? Hello Nathan, I am also interested by this feature and would be interested in APBS being able to print the result of this calculation. I am also interested into it being available for small molecules as well a proteins, if possible. Best regards, Francois. > Thanks, > > -- > Nathan Baker > Pacific Northwest National Laboratory > Phone: +1-509-375-3997 > http://nabaker.me > > From: Evelyne Deplazes <eve...@ho...<mailto:eve...@ho...>> > Date: Monday, February 11, 2013 3:26 PM > To: APBS-USERS mailing list <apb...@go...<mailto:apb...@go...>> > 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 > > ------------------------------------------------------------------------------ > Free Next-Gen Firewall Hardware Offer > Buy your Sophos next-gen firewall before the end March 2013 > and get the hardware for free! Learn more. > http://p.sf.net/sfu/sophos-d2d-feb > _______________________________________________ > apbs-users mailing list > apb...@li... > https://lists.sourceforge.net/lists/listinfo/apbs-users > |
From: Baker, N. <Nat...@pn...> - 2013-02-14 01:44:51
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Hi Francois -- Thanks for the feedback! Steven, is this something that you could work on? Thanks, -- Nathan Baker Pacific Northwest National Laboratory Phone: +1-509-375-3997 http://nabaker.me On 2/12/13 8:41 PM, "Francois Berenger" <ber...@ri...> wrote: >On 02/13/2013 01:06 PM, 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/d8b8ef203030c0f4cfc8d98a58868f3824 >>0a490c/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? > >Hello Nathan, > >I am also interested by this feature and would be interested in APBS >being able to print the result of this calculation. > >I am also interested into it being available for small molecules >as well a proteins, if possible. > >Best regards, >Francois. > >> Thanks, >> >> -- >> Nathan Baker >> Pacific Northwest National Laboratory >> Phone: +1-509-375-3997 >> http://nabaker.me >> >> From: Evelyne Deplazes >><eve...@ho...<mailto:eve...@ho...>> >> Date: Monday, February 11, 2013 3:26 PM >> To: APBS-USERS mailing list >><apb...@go...<mailto:apb...@go...>> >> 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 >> >> >>------------------------------------------------------------------------- >>----- >> Free Next-Gen Firewall Hardware Offer >> Buy your Sophos next-gen firewall before the end March 2013 >> and get the hardware for free! Learn more. >> http://p.sf.net/sfu/sophos-d2d-feb >> _______________________________________________ >> apbs-users mailing list >> apb...@li... >> https://lists.sourceforge.net/lists/listinfo/apbs-users >> > > >-------------------------------------------------------------------------- >---- >Free Next-Gen Firewall Hardware Offer >Buy your Sophos next-gen firewall before the end March 2013 >and get the hardware for free! Learn more. >http://p.sf.net/sfu/sophos-d2d-feb >_______________________________________________ >apbs-users mailing list >apb...@li... >https://lists.sourceforge.net/lists/listinfo/apbs-users > |