From APBS calculation in VMD and PyMOL, we can easily construct a charged protein structure from their PQR file. Now, is it possible to obtain a pot.dx file from PQR file for a charged solid particle considering partial surface charge density? Any information will be helpful.
Since APBS needs a dfefinite type of molecular structure to solve, it is impossible to use it for nanoclusters itself. Thus it needs to be done in another way.
Sir, first and foremost, I would like to thank you for such an informative answer. I have written the PQR files for the uncharged nanoparticles and have obtained the gridded data of potential. Now, my problem is to superimpose the charge grid onto the nanoparticle pqr model. How can I able to do that? Please let me know. Thanks.
Thank you Sir. I have written down both the PQR file and potential isosurface using OpenDX by a custom build code, since APBS does not work in the present case (I think it holds good for only protein structures). The output through OpenDX visualizer shows that the isosurface bears the necessary signature of the charge distribution that obtained experimentally, as shown in the image attached. But, the hardest problem came thereafter, and I could not able to solve it. The .dx isosurface potential file generated through OpenDX could not be read through VMD, the data structure is not similar to that of the .dx file mentioned in APBS website and the fonts appeared pointing the coordinates in an unknown format that I could not able to read. Since OpenDX software supports are not available I could not ask for a solution to them. If there exist any other software apart from APBS to write out a .dx file? I have also found out a script which converts OpenDX files to a format that could be read by VMD, but that was not helpful either. If you kindly find me a solution, it will be a great help to me.
Sir, thank you for your continuous support that always bring me back from the delusion from being puzzled. I have gone through all the files you have sent to me, specially the pot.dx file. Was it written with APBS? Please let me know if there exist any other way to write the charge grid in .dx format instead of using OpenDX itself, because, after last 12 hours of work, the problem regarding the legibility of the data through VMD still persist. I am still looking out for a better and flawless way to write the code module, meanwhile I am sending you a representative dataset that I have created for your kind perusal. The dataset contains (1) charge grid data in format (.txt); (2) OpenDX code module (.net); (3) OpenDX input (.general); (4) PQR file for the uncharged nanoparticle. Looking forward for your kind reply that lead always to a solution.
I have tried to reconstruct my volumetric data file and got a regular pattern. Since the mesh is not enough simple, the grid size needs to be flexible to acoomodate suitable boundary. Since the charge grid comes up in the fashion of volumetric data, I have no option but superimpose the charge grid onto the PQR file, so as to assign the atomic charge, depending on the positional coordinates.
Last one month I have tried a lot to model the scattered volume data. I think now I might able to solve it through NumPy array fitting. I need some more strategies from your end, Sir. I need some more time to learn python.
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