Pavan K Madasu

9 Questions 16 Answers 0 Followers

Questions related from Pavan K Madasu

Can I perform alchemical free energy calculations for a Normal MD simulation?

I have a trajectory of MD simulation which is apt for doing free energy calculations by MM GBSA/PBSA methods. Can I use the same trajectory for alchemical free energy calculations or Thermodynamic...

12 April 2023 693 1 View

How to fix the following error while calculating MMPBSA?

I think it's the issue with the python version...Kindly drop your suggestions to fix the issue. Thanks in advance.

31 July 2022 810 0 View

Does Princiapal component Analysis performed on two trajectories of the same complex or different complexes?

To be clear, lets say I have a protein X which binds with a family of proteins Y (Y1, Y2,...). I wish to PCA for my amber production runs. Option 1: Can I do PCA for X-Y1 Prod1 vs X-Y1...

03 May 2022 6,797 0 View

How to generate fragment libraries for a protein sequence?

Hello everyone, I have a protein sequence without any associated/similar reported structures in PDB. So I have decided to proceed with Ab initio method using rosetta. Is it mandatory generate...

05 April 2022 9,328 3 View

If I wish to stop an MD simulation (AMBER) in between, what command I need to use to write/extract .rst file ?

#AMBER #StopSimulation

01 January 1970 9,170 3 View

Pucker distributions of Nucleic acids..

Usually the sugar puckers are either C2'endo or C3'endo...For C2'endo the angle lies between 100 and 200...What if the angles lies between 300 and 400...In which pucker state they are...

01 January 1970 3,776 0 View

Issue with MMPBSA protein-nucleic acid sytem?

My MMPBSA input file worked well with protein-ligand system but fail to work with protein-nucleic acid system. The input file is as follows: / &pb istrng=0.100, / I have made a subtle...

01 January 1970 9,968 0 View

Error in writing output file using Command Prompt (Auto Dock Vina)

I am using Autodock vina for docking. The following error recurring with my system. I can do the same by using other's laptops. Too what extent I have to depend on others? I wish to fix it. Please...

01 January 1970 6,564 2 View

Analysis of active site cavity size and SASA fluctuations of MD simulation trajectories.

Can you suggest me some similar tools and tutorials for the same. I have a protein with enzymatic activity. I wish to analyze the active site cavity size and SASA variations/fluctuations...

01 January 1970 9,752 0 View