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Questions related from Amali Guruge
My system contains three micelles. I want to calculate radius of gyration for each micelle in the system. I did the micelle clustering, but I am struggling with the step 3 in...
08 August 2018 2,662 1 View
Dear All, I want to arrange my surfactant molecules in a hexagonal arrangement for my MD simulation. Appreciate, if anyone can guide me to do that. Thank you.
07 July 2018 8,444 2 View
Dear All, My system contains water molecules and polyethylene glycol molecules. I generated the box (15.2*15.2*15.2 nm*3) using genbox command. Thereafter, PEG molecules were added using gmx...
10 October 2017 7,093 0 View
Dear All, In my MD simulation I only added counter ions (20 Na+ ions) to neutralize the system. Now I want to do MM_PBSA calculations for my MD runs using g_mmpbsa. In order to do perform polar...
07 July 2016 7,565 1 View
Dear All, I want to get high quality images of 2D pictures generated by PoseView software. Can anyone help me? Thank you.
06 June 2016 6,150 1 View
Dear All, I want to do molecular docking processes for an enzyme and ligands in the presence of co-crystallized water molecules (of the enzyme) using DOCK6. Can anyone help me? Appreciate if...
06 June 2016 2,638 0 View
Dear All, I completed molecular dynamics for three ligands, T1L25, T2L25 and T3L25 using GROMACS software with CHARMM27 force field. How can I explain the rmsf behavior of linker domain (linker...
04 April 2016 5,125 5 View
Dear All, I have two receptor-ligand complexes. In one system, the ligand intercalates in DNA and from two hydrogen bonds (one with the enzyme and one with DNA duplex). In other system, the ligand...
03 March 2016 352 4 View
Dear All, I used SwissParm to generate CHARMM itp files for my ligand molecules. I used GROMACS for molecular dynamics simulations. After getting the itp file for the ligand, I used that file...
12 December 2015 3,633 0 View
Dear all, Currently I am trying to do molecular dynamics simulations for human topoisomerase I enzyme. I am using GROMACS software with CHARMM forece field. I want topology file for my ligand...
11 November 2015 6,703 2 View
I want to convert the pdb format of topoisomerase I into Gromacs.The pdb id for the structure is 1K4T. I removed ligands, water and Hg ion from 1K4T. But DNA is required for the MD simulation. I...
09 September 2015 5,114 1 View
I completed 30 ns long (30 ns long simulation can divide in to six 5 ns simulations) molecular dynamics simulation for an enzyme-ligand complex. Now I want to visualize structural changes in each...
06 June 2015 751 2 View
