Tarak Karamakar

10 Questions 25 Answers 0 Followers

Questions related from Tarak Karamakar

How would I get the converged free energy profile for an open-closed transition in an enzyme?

I am studying an enzyme where the closing of a loop should happen upon ligand binding to the active site. In unbiased simulations, even after 300 ns of simulation time the loop does not close the...

10 June 2016 7,363 9 View

Are CGenFF parameters (from ParamChem) for peptide analogues good enough to couple with Charmm36 parameters for the lipids in a membrane?

I need a suggestion related to simulation of peptide-membrane system. I've got tentative CGenFF parameters for the peptide analogues from ParamChem with charge and param penalties 35 and 53...

04 February 2015 9,138 1 View

Is it possible to assign a particular charge (restraint) on an atom during RESP calculation using REDTools?

I'm trying to calculate RESP charges of atoms in a complex system. I need to keep a fixed charge on certain atoms during the charge calculation. Is there any such procedure in REDtools or REDserver?

22 January 2015 8,146 3 View

Could any one help me in generating a residue-residue contact map?

I need to generate a residue-residue contact plot for a protein. I was trying in VMD but there I didn't find a way improve the quality of the plot, I mean a way to include the residue indices,...

08 November 2014 4,341 4 View

Can someone comment on covalently bound ligand parametrization?

I have a protein, where one of the reaction intermediate is covalently attached with a residue inside the active site. I need to parametrize this part of the protein. I used standard RESP...

15 July 2014 5,966 3 View

Can someone advise on protein-protein interaction energy in a dimer?

Could anyone guide me to analyze protein-protein interaction energy in a MD trajectory? I'm simulating a dimer and want to see the interaction energy between the two monomers. Is it the same way...

02 May 2014 2,784 3 View

What is a suitable box size for a molecule, described in quantum mechanics, in a QM/MM simulation?

Is it the box which can only contain the molecule or I can use a bit larger box for the same?

18 December 2013 4,655 6 View

Homodimer protein simulations?

While simulating a homodimer I see that the active site of one monomer is very stable, the orientation of ligand molecules and the nearby protein residues are well close to the crystallographic...

20 August 2013 4,344 34 View

Gromacs CPMD QM/MM versions

I am planning to perform a QM/MM calculation of my protein system. Can anybody tell me whether gromacs-4.5.5 can be patched with the latest version of CPMD? If not, then please suggest some...

12 August 2013 4,450 3 View

Does anybody know the effect of water molecules, present with the protein pdb structure, on the APBS electrostatic calculation in PYMOL?

I'm getting two different types of electrostatic potential maps in presence, and in the absence of water molecules.

12 May 2013 2,032 2 View