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 8,395 1 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 8,411 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 6,004 2 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 1,212 3 View

How to analyze a particular region of my simulation box in GROMACS?

Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...

03 March 2021 9,989 2 View

After a reference from Int J Body Compos Res, can any body help?

Hi, I am after the reference below, my library says it cannot obtain a copy either locally or internationally, any help appreciated! Chris Wang ZM, Heshka S, Wielopolski L, Pi-Sunyer FX, Pierson...

03 March 2021 6,193 1 View

Irradiation data for JAPAN?

Hi, Could you help me to get the latest (2019, 2020) solar resource data for a particular site in JAPAN? PV GIS and NSRDB data are not in reach to JAPAN, I'm looking for some other database for...

03 March 2021 961 3 View

Can we distinguish the type of free fluid inside the pelvic and abdominal cavities whether blood or serous fluid using the ultrasound?

during ultrasound examination of acute abdomen, sometimes we see free fluid , can we know the type of fluid ,whether blood or not , using ultrasound only? if yes , what are the sonographic...

01 March 2021 7,476 4 View

How can I calculate the rdf of water molecules around 'Na' ions that are closest(adsorbed) to the nanoparticle(solute)?

Hi, I want to calculate the radial distribution function for water molecules around the Na+ ions adsorbed on the surface of a spherical nanoparticle using the gromacs trajectory dynamically? For...

28 February 2021 5,650 1 View

How to calculate Ligand-active site distance in a ligand-protein complex from MD simulation?

I have run a MD simulation of a ligand-protein complex in GROMACS using CHARMM forcefield. Reviewer has asked me to calculate Ligand-activesite distance and binding free energy of ligand with...

27 February 2021 4,703 1 View

How can I assign a velocity along one direction to CO2 molecules in a molecular dynamics simulation using GROMACS?

Dear all, I am trying to perform a MD simulation about the interaction between CO2 and a polymer. I create my model, solvate it and perform the NVT and NPT equilibration. Now I am not able to...

26 February 2021 10,014 3 View

How does GROMACS calculate the average structure of proteins?

I want to get a average structure from a pdb file containing multiple models. I used the command below: gmx cluster -f input.pdb -s topol.tpr -cutoff 20 -method gromos -av GROMACS...

25 February 2021 6,314 1 View

Why do the air flow results vary totally when adding scalar in CFD ?

Dear All, We are using Autodesk cfd to calculate the air flow in a single sided naturally ventilated room, where air flow depends only on buoyancy due to temperature difference between inside and...

25 February 2021 9,602 4 View

Is there an open source free software for text mining and sentiment analysis?

I am looking for a free software for text mining and sentiment analysis for my research on customer review mining (it involves calculating polarity of attributes,opinion oriented information...

25 February 2021 1,920 6 View