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Questions related from Srinivasa Rao Penumutchu
I followed the below instructions to install Gromacs-5.1.4 after patching up with plumed. and then ran gromacs-plumed simulations end up with following errors. I didnt see any errors, while...
08 August 2017 8,618 0 View
We solved the RNA structure using NMR. we would like to refine the structure using Gromacs or amber. does anyone know that how to convert the xplor distance restraints/dihedral to Gromacs...
03 March 2015 4,488 3 View
I finished docking based on NMR data and MD simulations using Gromacs . I would like to know that What kind of data should be provide from simulations to explain or confirm the multiple...
01 January 2014 8,093 1 View
We did the Gromacs MD simulation for the protein complex , the complex is stable during 15 ns Simulation. We would like to plot the interface area plot for the protein complex along the entire...
12 December 2013 10,079 6 View
Could anyone provide references or protocols to measure the binding affinity by using fluorescent ligand with protein? Ligand shows fluorescence excitation/emission: 270/340 nm.
11 November 2013 2,990 10 View
I would like to setup unrestrained MD simulations on gromacs for protein-protein complex . The protein complex was calculated by HADDOCK by using NMR Chemical shift restraints? Could you please...
03 March 2013 8,473 2 View
I would like to calculate the number of water molecules replaced before and after complex formation on the binding surface? How we can do this? Any suggestions?
12 December 2012 4,235 8 View
I am new to MD simulation for Protein - protein complex , sorry for asking some basic questions ! 1. What Kind of information it will provide if I do MD simulation for protein complex after...
10 October 2012 9,906 2 View
