Nitin Sharma

8 Questions 32 Answers 0 Followers

Questions related from Nitin Sharma

Is an MD simulation for a tetramer equal to 4 simulations of a monomer?

I know that multiple MD simulations are good for statistics and increases the reliability of the results. I have a protein which is tetrameric in natural state. i would like to know whether I...

04 April 2014 8,557 4 View

Can anyone help with Idecomp AMBER?

Idecomp Energy decomposition scheme to use: 1 - Per-residue decomp with 1-4 terms added to internal potential terms 2 - Per-residue decomp with 1-4 EEL added to EEL and 1-4 VDWadded to...

04 April 2014 5,287 0 View

Can anyone help with predicting the binding pose MD or simulated annealing?

I want to explain activity of ligands (IC50 already determined) by binding pose, As per my experience docking is prediction capacity of docking is very poor and i am unable to explain results....

04 April 2014 7,895 1 View

Can someone explain what the internal distance in a protein and also in general is?

Internal distance in a protein....

03 March 2014 1,983 3 View

Any advice on this error in extending simulation from .rst file _ AMBER?

I have an error in extending simulation from a 50ns MD run restart file . ERROR: I could not understand line 11876 -0.0694812 -0.0371947 -0.0775758 0.2710202 -0.5647205 -0.7658839 Lines...

02 February 2014 7,557 0 View

Does anyone have experience with selecting final pose after MD simulation?

I have been doing a lot of MD simulation lately but i am confused how to select the final pose for the ligand in the system. Several approaches I can think of are : 1) cluster the ligand and...

01 January 2014 7,037 19 View

Can a compound with IC50 more 100 uM have a negative binding free energy?

I have two compounds first one i.e.CompA having IC50 of about 11uM and another one i.e. CompB with IC50 greater than 100 uM resulting in CompA as active compound and CompB as inactive compound. I...

01 January 2014 6,590 6 View

Optimizing ligands before running molecular dynamics simulation?

Is it necessary to optimize geometry before molecular dynamics simulation? I am using AMBER for MD simulation. I have seen studies where ligand was parameterized according to quantum chemical...

01 January 2014 1,822 17 View