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Questions related from Vishal Pandya
I have a system with two proteins and a membrane as following protein-1, protein-2, and membrane bilayer. I would like to know whether the protein-2 binds first to protein-1 or the membrane to...
07 July 2018 10,049 1 View
I would like to validate a homology model. After peroforming MD simulation, one way is to check the stereochemical quality, Ramachandran plot, dssp, B-factor, etc and map the model with the...
07 July 2018 6,208 11 View
I would like to set the default background in vmd as gradient. Therefore I tried the following method to set default background gradient in ~/.vmdrc file but that did not work. Could anyone please...
06 June 2018 9,787 2 View
I have installed VMD 1.9.2 on Ubuntu machine and when I try to change the representation from lines to cartoon the GUI becomes very slow and one can feel like VMD is not working. It does not slow...
08 August 2017 594 10 View
Hi all, Is there a way to find consistent hydrogen bonds in between sidechain-sidechain, backbone-backbone residues in gromacs? Can I point out some residues and plot a graph wherein I can see...
08 August 2017 1,483 4 View
Is there anything like universal 3 letter code for sulfonated tyrosine like other usual amino acid residues
08 August 2017 4,160 2 View
Suggestions regarding Protonation prediction servers apart from H++., PDB2PQR and Reduce!
05 May 2017 3,103 4 View
While making movie of GROMACS trajectory in VMD, How one can stop motion of protein going from one direction to the other in PBC box?
09 September 2016 8,240 0 View
