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Questions related from Tarak Karamakar
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...
06 June 2016 6,324 12 View
Dear All, I need to impose a distance restraints between COM of protein active site residues and COM of a ligand. But the problem is I am using an .itp file generated from acpype. While I use the...
07 July 2015 4,896 0 View
I would like to model three missing loops in a protein. Unfortunately, there is no similar protein having these missing residues (template is not available). I tried to use FALC-Loop server, but...
05 May 2015 2,481 11 View
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...
02 February 2015 8,370 1 View
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?
01 January 2015 10,078 4 View
Projection of trajectory onto first two eigenvectors- Does it mean that i) the superposition of molecular structures (a set of C-alpha coordinates) over a trajectory are projected onto a plane...
12 December 2014 4,559 2 View
I am getting a B-factor difference of ~250 A^2 between X-ray structure and simulation (8pi2 msf/3), plot is attached. The overall trend is in good agreement with the crystal structure. Generally,...
12 December 2014 598 13 View
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,...
11 November 2014 9,121 5 View
While simulating a protein-ligand complex, during equilibration the 5'-phosphate group of it is coming out of its binding pocket. Few water molecules are crawling in. I have performed two...
11 November 2014 3,319 10 View
I see a flexible loop opening from a protein after removal of the ligands from the active site (Molecular Dynamics simulations). I expect that the reinsertion of the same ligand molecules in the...
08 August 2014 6,320 3 View
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...
07 July 2014 4,057 4 View
We calculated the interaction energy of a system in two methods, B3LYP/aug-cc-pVTZ (Gaussian) and SAPT2+3/aug-cc-pVTZ (PSI4) and got an energy difference of about 8 kcal/mol. How reliable this is?
07 July 2014 628 7 View
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...
05 May 2014 2,006 4 View
Need little suggestion regarding the effect of non-active site mutants on enzyme activity: How to approach to this issue by means of molecular dynamics simulations? What are the appropriate...
04 April 2014 186 13 View
I'm trying to perform a QM/MM simulation in CP2K by taking the well equilibrated (seeing the tot_eng, pot_eng, temperature) configuration obtained from classical simulation in NAMD with charmm...
03 March 2014 6,976 0 View
A protein has been proposed to have an alternative ligand binding mode. The ligand coordinates in this mode for this protein is not known by experiment. However, pdb strcuture of a similar protein...
02 February 2014 5,957 14 View
Is it the box which can only contain the molecule or I can use a bit larger box for the same?
12 December 2013 8,393 6 View
Has anyone performed any kind of QM/MM simulations in gromacs-4.5.5, and in latest version of CMPD?
09 September 2013 9,857 0 View
How to include the title of papers in my reference list? I'm preparing the manuscript in Latex and following the JPC B style. In the main TeX file I use the following...
09 September 2013 8,627 6 View
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...
08 August 2013 9,427 3 View
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...
08 August 2013 7,802 35 View
I carefully looked at the trajectory (VMD movie) and saw there are two flexible terminii fluctuating with a very high amplitude contributing to the high value of RMSD. Should I report this problem...
06 June 2013 5,682 10 View
Can anyone comment on the reliability of the parameters generated from SWISSPARAM server? I read few of them, saying that the parameters are good enough to start with. Thanks
06 June 2013 2,013 3 View
I'm getting two different types of electrostatic potential maps in presence, and in the absence of water molecules.
05 May 2013 1,154 2 View
I want to perform a free energy calculation on a dihedral, rotating from zero to +pi not -pi to +pi. I am using plumed + gromacs for my calculation. Can anybody suggest how to put this colvar limit?
04 April 2013 5,010 0 View
