How to calculate energy of a protein-ligand complex?

More Dimuthu Kodituwakku's questions See All

How to build a topology for a novel molecule in CHARMM?

Hi, I'm trying to attach a carbonyl linker to Lys so that I can attach a PEG molecule to it. I have attempted so far by combining Lys , N-terminal and C-terminal topology data . But I'm having...

24 August 2020 8,474 1 View

How to simulate a protein with FAD using amber?

My protein (GoX) contains a FAD coenzyme which is important for protein's function. How do I simulate this protein using amber as it does not provide force fields for co-enzymes?

01 March 2020 4,826 3 View

How to combine a ligand and protein topology file in NAMD?

I'm fairly new to NAMD. I have generated a topology file for my ligand through CGENFF but I do not know how to combine topology files of ligand and the protein.

26 January 2020 8,463 1 View

Can double bonds get converted to single bonds during an MD simulation?

I have performed an MD simulation for 10 ns. After going through output pdb files I found that my 2 double bonds have been converted to single bonds? Is that possible?

16 October 2017 6,058 2 View

How to view ligand-protein non bonded interactions from discovery studio?

I have an output file of a molecular dynamics simulation for a protein-ligand complex. But I can't view the ligand through DS visualizer. It says my ligand is undefined.

08 October 2017 3,027 9 View

Which method of RMSD calculations is the best for protien analysis?

I have performed an MD simulation for a protein-ligand complex for 10ns. Now I need to analyze the effect of ligand binding and MD simulation on the protein structure. Which RMSD method is the...

06 October 2017 1,265 3 View

Is there any research topics related to machine learning/reinforcement learning? (a simple project)?

This is for my final year research project. Im following a degree in Information Technology

18 February 2017 9,712 3 View

Can you suggestion PhD topic relevant household finance and sustainability including relevant theories

I would like to read PhD relevant to household finance and sustainability. Plz share your research ideas, including relevant theories

01 January 1970 5,261 6 View

Which Scopus Journal provides the most affordable fees?

"PUBLISHING IN A SCOPUS JOURNAL" Researchers are now at a cross road. The critical need to publish in a Scopus or ISI, etc journal is ever vital. Journal Publication fees must be submitted....

10 August 2024 8,621 1 View

How to develop investments in renewable energy sources?

08 August 2024 5,112 3 View

GC-MS retention index prediticon?

Hello experts, Does anyone know any free software about retention index prediction ?

08 August 2024 7,403 2 View

Gromacs first step of minimization ?

I have face this problem anyone help me how to solve this issue ?which is below Fatal error: There are inconsistent shifts over periodic boundaries in a molecule type consisting of 78 atoms. The...

07 August 2024 2,598 1 View

Could you please suggest methods to compare free protein and immobolized protein binding properties?

I have an antibody binding generic protein and I need to compare its activity in a free and immobolized form. I understand that there are a number of methods to determine Kd value of a free...

05 August 2024 5,311 0 View

Where can I find free research instruments for Nursing?

for eg. transition shock scale

01 August 2024 5,998 0 View

Why do open and free science in a world where science is not open and free?

Because I have realized that the world tends more and more to do open and free science and there is a trend more and more to choose free databases, free tools and open access platforms.

01 August 2024 10,046 1 View

Is artifacts in XPS possible to build high deviation in binding energy larger than 5 eV??

Hello. Thanks for your consideration to see my question. Recently, I conducted XPS anaylsis of g-CN that is prepared from thermal polycondensation of DCDA, so-called conventional bulk-g-CN,...

30 July 2024 9,824 2 View

How to restart MD without using checkpint file in GROMACS?

Dear All Gromacs User I would like to restart MD without using checkpint .cpt files? I heard there is a way for acheiveing this. Any input and sugegstions are most welcome. Thanking You Budheswar

29 July 2024 3,084 8 View

Is there a database with onshore wind production for the wind farms in Portugal?

I am looking to predict some production for future onshore wind energy production in Portugal, is there any database with info of performances of the existing wind farms in the country? something...

28 July 2024 1,750 1 View