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Questions related from Uttam Kumar Basak
It is often necessary to know the parameters of Lennard-Jones (LJ) potential for various atoms. There may be database for LJ parameters. I am just curious to know how these parameters are obtained...
18 January 2016 9,669 11 View
I have a 2D system, you can think of it as a 2D sheet. There is a formation of ridges in this sheet when it is given a constant in-plane pressure. I want to model the ridge dynamics. Is there any...
25 July 2014 1,669 3 View
I want to calculate interaction energy between two molecules as a function of their separation. I also want to see how geometry of the molecules affects their interaction energy. Can you suggest a...
25 May 2014 1,699 16 View
I have obtained free energy of solvation in water using perturbation method with GROMACS. I want to calculate the solubility of the molecule in water. How can I do that?
14 January 2014 5,280 34 View
Antechamber from AmberTools13 is giving an error: " cannot run "..../sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit" " I have installed AmberTools13...
21 August 2013 3,981 7 View
I need a 3D structure of molecule for molecular dynamics simulation. I don't have a good chemistry background. I want a software which can assign the bond length, bond angle etc. automatically....
12 August 2013 6,527 10 View
I have used ATB (http://compbio.chemistry.uq.edu.au/atb/) server to generate topology for piroxicam molecule (having 36 atoms). It has generated topology for GROMOS96 force field with two charge...
07 August 2013 2,370 6 View
I have a .mol 3d structure of a nonligand molecule (piroxicam). I opened it in pymol and added hydrogens to it before saving it as .pdb file. Then I used this file as an input to ATB...
29 July 2013 4,999 5 View