Re: [apbs-users] Query on calculating charge density of DNA
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Re: [apbs-users] Query on calculating charge density of DNA
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From: Nandigana, V. V. R. <nan...@il...> - 2013-07-05 22:02:52
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Hi Nathan, 1. I have looked at your value.c file and understood how the trilinear interpolation was done. I wrote a small c code and implemented the interpolation algorithm myself and was able to obtain the charge density for the DNA. 2. I have another question. Currently, I have mapped the DNA structure (converted .pdb file into .stl file) inside my solid state nanopore membrane and meshed it. Also, I have the charge density of the DNA mapped at each grid point. I am currently solving for the Poisson-Nernst-Planck equation over the entire domain (DNA+solid state nanopore) to determine the ionic charge density distribution inside the membrane in the presence of the DNA. For the Poisson equation, the source term includes the charge density of the DNA and the charge density of the ions, and I have considered dielectric permittivity of water = 80 inside the membrane and 2.0 for the DNA. However, while solving for the Nernst-Planck equation, I would like to know how do we ensure that there is no ions at the points where DNA is present. In other words, how do we ensure that the ions do not penetrate the DNA structure. Please let me know your suggestions. Thanks Regards, Vishal ________________________________________ From: Baker, Nathan [Nat...@pn...] Sent: Tuesday, June 25, 2013 9:16 PM To: Nandigana, Vishal Venkata Raghave Cc: apb...@li...; Stevens, Andrew J (PNNL) Subject: RE: [apbs-users] Query on calculating charge density of DNA Hello – I’m Cc’ing Andrew Stevens to help answer your questions. If you are familiar with linking to the APBS libraries, you should be able to call the Vgrid_value() function directly for your application. Thanks, __________________________________________________ Nathan Baker Pacific Northwest National Laboratory Tel: +1-509-375-3997 http://nabaker.me<http://nabaker.me/> From: nan...@gm... [mailto:nan...@gm...] On Behalf Of nandigana vishal Sent: Tuesday, June 25, 2013 3:46 PM To: Baker, Nathan Cc: apb...@li... Subject: Re: [apbs-users] Query on calculating charge density of DNA Thanks, Nathan. I have looked at the multivalue.c file. 1. The comments section mentions that the value at the intermediate grid points is interpolated using trilinear interpolation. However, I do not see any interpolation code. Is there any inbuilt function the program calls for the interpolation. 2. Also, how do we compile and execute this program. I see the executable file of multivalue in my ~/APBS-1.4-linux-static-x86_64/share/apbs/tools/bin. However, when I run the program using the following command multivalue DNA_data0.0.csv DNA_charge.dx DNA_new_mesh I get the following error. multivalue: command not found 3. Also, I could not find any apbscfg.h and vclist.h files which was necessary for compiling multivalue. Please let me know where can I find these files and how to execute this program. Thanks for the help On Mon, Jun 24, 2013 at 8:57 AM, Baker, Nathan <Nat...@pn...<mailto:Nat...@pn...>> wrote: Hi Vishal – You could use the multivalue program (http://www.poissonboltzmann.org/apbs/user-guide/apbs-tools/multivalue) distributed with APBS to do this but it may not be the most efficient mechanism. However, it might be useful to use this program’s code as a starting point for your own. Thanks, __________________________________________________ Nathan Baker Pacific Northwest National Laboratory Tel: +1-509-375-3997<tel:%2B1-509-375-3997> http://nabaker.me<http://nabaker.me/> From: nan...@gm...<mailto:nan...@gm...> [mailto:nan...@gm...<mailto:nan...@gm...>] On Behalf Of nandigana vishal Sent: Sunday, June 23, 2013 10:53 AM To: Baker, Nathan Cc: apb...@li...<mailto:apb...@li...> Subject: Re: [apbs-users] Query on calculating charge density of DNA Thanks, Nathan. I have now the grid points and the corresponding DNA charge density from APBS. Also, I have the grid points of the DNA structure generated in my solver. I would like to map the DNA charge density from APBS generated grid points onto my solver. I would like to know if there are any codes available to do this mapping, or should I write a small script to map them using interpolation techniques. Thanks Regards, Vishal On Fri, Jun 21, 2013 at 1:00 PM, Baker, Nathan <Nat...@pn...<mailto:Nat...@pn...>> wrote: Hello -- In addition to isocontours, cut-plane slices with contour plots might also be useful. I would recommend using the mesh lengths and dimensions generated by PDB2PQR. Thanks, -- Nathan Baker Pacific Northwest National Laboratory +1-509-375-3997<tel:%2B1-509-375-3997> http://nabaker.me On 6/19/13 3:40 PM, "Nandigana, Vishal Venkata Raghave" <nan...@il...<mailto:nan...@il...>> wrote: >Hi Nathan, > >Yes, I have considered VMD to visualize these results. I was visualizing >it using isosurface drawing method. I would like to know what other >drawing methods would you recommend. Also, I wanted to know, in order to >get an accurate description of the potential and charge density map of my >DNA structure, what should be an approximate mesh size that should one >should start with. I am using a sspoly(dA)40 DNA structure. > >Please let me know. > >Thanks > >Regards, >Vishal >________________________________________ >From: Baker, Nathan [Nat...@pn...<mailto:Nat...@pn...>] >Sent: Wednesday, June 19, 2013 4:26 AM >To: Nandigana, Vishal Venkata Raghave; apb...@li...<mailto:apb...@li...> >Subject: Re: Query on calculating charge density of DNA > >Hello -- > >Have you considered using VMD, PyMOL, or PMV for this visualization >application? > >Thanks, > >-- >Nathan Baker > >Pacific Northwest National Laboratory >+1-509-375-3997<tel:%2B1-509-375-3997> >http://nabaker.me > > > > >On 6/16/13 8:26 PM, "Nandigana, Vishal Venkata Raghave" ><nan...@il...<mailto:nan...@il...>> wrote: > >>Thanks, Nathan. I read the documentation for OpenDx and installed the >>software. >> >>I ran a few tutorials for OpenDX and understood the implementation >>procedure of the software. However, when I tried to view the results of >>the potential and DNA charge density after execution of APBS, I got weird >>results. Attached please find the DNA charge density result obtained from >>OpenDX visualization and the APBS.in file of my test case. >> >>I had followed the step 3 given in the following tutorial to view the >>results >>(http://www-lsp.ujf-grenoble.fr/recherche/a3t2/a3t2a2/bahram/OpenDX/). >>In other words, the results were obtained using the .general file >>generated by the dx software. Using the .general file, I opened the >>visual program editor and constructed three objects on the canvas to >>visualize the results. The three objects were: Import->Autocolor-> Image. >> >>Please let me know if this implementation is correct. If not, please let >>me know the correct procedure to visualize the charge density and >>potential maps of the APBS output using OpenDX software. >> >>Thanks >> >>Regards, >>Vishal >>________________________________________ >>From: Baker, Nathan [Nat...@pn...<mailto:Nat...@pn...>] >>Sent: Wednesday, June 12, 2013 8:34 AM >>To: Nandigana, Vishal Venkata Raghave; apb...@li...<mailto:apb...@li...> >>Subject: RE: Query on calculating charge density of DNA >> >>Hello -- >> >>Please see the documentation at >>http://www.poissonboltzmann.org/apbs/user-guide/running-apbs/input-files/ >>e >>lec-input-file-section/elec-keywords/write and >>http://www.poissonboltzmann.org/file-formats/mesh-and-data-formats/opendx >>- >>scalar-data. >> >>Thanks, >> >>__________________________________________________ >>Nathan Baker >>Pacific Northwest National Laboratory >>Tel: +1-509-375-3997<tel:%2B1-509-375-3997> >>http://nabaker.me >> >> >>-----Original Message----- >>From: Nandigana, Vishal Venkata Raghave [mailto:nan...@il...<mailto:nan...@il...>] >>Sent: Tuesday, June 11, 2013 6:07 PM >>To: Baker, Nathan; apb...@li...<mailto:apb...@li...> >>Subject: Query on calculating charge density of DNA >> >>Dear Nathan, >> >>I am currently using APBS to calculate the charge density on each grid >>point of my DNA structure. I used the following command in the APBS.in >>file to dump the DNA charge. >> >>"write charge dx DNA_charge # Write out DNA charge density". Also, I >>have the following number of grid points. >>"dime 97 97 321". >> >>I found that after running APBS, I got a matrix for the DNA charge >>density of size: 1006763*3. Now, I would like to know, how to correlate >>this with the mesh points. Please let me know the APBS output style >>format. >> >>Thanks >> >>Regards, >>Vishal > ------------------------------------------------------------------------------ This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev _______________________________________________ apbs-users mailing list apb...@li...<mailto:apb...@li...> https://lists.sourceforge.net/lists/listinfo/apbs-users -- Regards Vishal Nandigana Graduate Student, Mechanical Engineering University of Illinois at Urbana Champaign, Beckman Institute for Advanced Sciences Room no - 3213, Illinois 61820, U.S.A. ------------------------------------------------------------------------------ This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev _______________________________________________ apbs-users mailing list apb...@li...<mailto:apb...@li...> https://lists.sourceforge.net/lists/listinfo/apbs-users -- Regards Vishal Nandigana Graduate Student, Mechanical Engineering University of Illinois at Urbana Champaign, Beckman Institute for Advanced Sciences Room no - 3213, Illinois 61820, U.S.A. |