Interaction map for protein-ligand particularly for calculating non-specific electrostatic interactions ?

19 February 2024 1 191 Report

Hello all,

I want to calculate interaction map for protein-ligand binding. This is to identify interactions, particularly the role of non-specific electrostatic interactions existing between the protein-ligand during the md simulation trajectory obtained using NAMD. Can anyone please guide me with steps to calculate it?

Aashish Bhatt

you can use NAMD energy.

https://www.youtube.com/watch?v=GbZHhCGCDMs&ab_channel=AOWANG

Badges
Science topic

More Farindra Kumar's questions See All

Which is the most efficient etching solution for nickel based alloys?

Which solution reveals the microstructure and features of nickel-based alloys?

02 March 2021 2,221 3 View

Which is the most convenient manufacturing software for Additive Manufacturing?

Which tools can be used to generate machine codes for additive manufacturing?

02 March 2021 7,220 2 View

Which is the best place in the world for the plant biotechnology research?

I am searching for a good place for the Post Doc,

02 March 2021 4,053 3 View

Which SAR dataset to use for generating coherency matrix and performing target decomposition (Description) ?

Working on chandrayaan-2 DFSAR data, there are three datasets available: 1) Slant range image data product: The slant range complex image file. Each pixel is represented by two 4-byte floating...

02 March 2021 8,481 3 View

How does one access the Cranet survey data on HRM practices?

Hello, The Cranet website does not provide any lead to the data obtained from their multinational survey on HRM practices. Any help on accessing the data would be most appreciated. Thank...

01 March 2021 9,536 3 View

Genome-wide gene identification protocol ?

Is there any book chapter/book, webpage or research article available to understand genome-wide gene identification?

28 February 2021 8,095 1 View

Can the problems of overfitting be solved without cross validation?

For an overfit data set the cross validation error will be much bigger than the training error. Is it true or false?

23 February 2021 3,616 2 View

Research Gate Does it help researches to publicize their scientific work ?

In my opinion, the RG site is useful in solving scientific problems and shows the researcher's ability. Besides, the separation of the H-index from the self-citations and the overall index is an...

22 February 2021 3,894 6 View

How to Study a proton NMR of Graphene prepared by Electrochemical Exfoliation technique?

I performed a Proton NMR of graphene powder prepared by electrochemical exfoliation technique. It shows some peaks. But I can't understand it.

21 February 2021 8,947 3 View

How to classify and recognize unseen image class in document sorting?

To sort the scanned document image I have to determine the class of document. But no of classes of image will keep on adding even after training. So at time of inference first I will detect unseen...

16 February 2021 4,501 3 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

What kind of fluid could I use for a pitfall trap that also does not invalidate molecular testing?

Hi, I want to start testing pitfall trap to obtain ants samples, but I need to conduct molecular analysis on those insects. So, what kind of fluid can I use? Ethanol expires too early and I need...

03 March 2021 5,978 5 View

Arena simulation - how do i model the following model in ARENA (see description) (new to ARENA)?

Hello, I'm fairly new to ARENA and I have the following problem: I have two queues in which, in each queue, a different order type arrives (both having an arrival rate of exponential 10). Order...

02 March 2021 2,431 3 View

Why are the velocities so high in my Boussinesq approximation Fluent simulation?

Hello, I have a mechanism where air rises due to convective flows. In this simulation, nothing is driving the air except this. I understand that the Boussinesq approximation only works for small...

02 March 2021 4,910 3 View

How to repeat an operation on an atom selection for multiple times in PyMol?

Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...

02 March 2021 4,569 4 View