Dr. Rohan Meshram

9 Questions 29 Answers 0 Followers

Questions related from Dr. Rohan Meshram

How to include entropy contribution in MMGBSA/MMPBSA results?

I have performed MD simulations and obtained binding free energy using MMGBSA. Say it was -30 Kcal/mol. Later on, I separately computed entropy (T-Delta-S) for the same system. The said entropy...

27 March 2025 2,036 0 View

What is the exact difference between restart files and restart.old files generated as output during NAMD simulations?

When one Performs MD simulations using NAMD. It generates restart files coordinates (.coor), velocity (.vel) and xsc (.xsc) files. It also generates restart files with extension .old. My question...

19 September 2019 5,628 3 View

What causes skin blackening in visceral leishmaniasis?

I am curious about the reason for blackening of skin during infection of leishmania donovani? Is it due to accumulation of some pigment or something else? If it is due to pigmentation then what...

22 February 2015 6,025 8 View

Regarding amino acid nomenclature, are there are software or codes that revert alternative names of Histidine (HSE/HID) to normal HIS?

I have a molecular dynamics trajectory and I wish to perform further study on the last frame. While generating PSF and during course of MD simulation, NAMD and VMD changes 3 letter code of...

02 November 2014 4,289 5 View

Why are binding free energy values calculated during molecular docking negative?

I just got curious to know what the significance of preferring a pose with more negative value is? What exactly does this negative sign signify?

17 July 2014 4,306 9 View

How to generate complex of protein and inhibitor pose obtained from docking using PyRx?

This question is quite relevant for people working on AutoDock using PyRx. It generates dlg files and provides binding free energy values. But it seems to be a dead end if one wish to generate...

02 June 2014 7,277 8 View

Why has the Human COX2 structure not been experimentally solved until now?

My work being centered around structure based drug design,I have always wonder what might be the exact reason behind the unavailability of structural model of human COX 2 (gene PTGS2). By that I...

27 May 2014 2,585 4 View

Does anyone have suggestions regarding virtual screening?

My initial compound library had 348,276 compounds. After applying various filters like functional group filters, Physio-chemical filters, removing duplicate compounds, removing Pan Assays...

19 February 2014 8,340 6 View

How to improve the performance by using NAMD for MD on windows OS?

I am using NAMD for MD on windows OS, using +p4 in "+p"On i5 processor uses 100 % CPU but not 100 % memory. How can we make 100% memory utilization?

19 November 2013 5,176 2 View