How to calculate pH of Protein structure?

Dear All, I want to do constant pH MD for an enzyme. For the analysis, I want to know, is there any way to calculate pH of static pdb structure? I have pKa (individual residue) and charge (whole...

02 March 2018 4,107 8 View

Sodium ion channel structure?

Dear all, For my research, I need the 3D structure of the sodium channel. Can anyone guide me how to make the complete strucutre for sodium channel?

02 March 2016 8,634 1 View

What is the protocol for studying the Molecular Dynamics of Drug Entry and binding with protein?

Dear All, I want to if there is any protocol available to simulate and analyze the entry of a drug to a binding pocket of a protein as well as binding at that position. All I could find is the...

08 September 2014 4,619 3 View

How do computers Visualize chemical structure?

Can someone please explain how computers identify rings and chains (and complete structure) from a Coordinate file (PDB or Mol2)?

03 April 2014 2,729 5 View

Publishing Articles as Student: Is it really impossible?

My team and I finished a couple of projects in Cancer informatics (Drug Designing). We want to publish them now, but, a fairly good computational bioinformatics journals, were quoting us a hefty...

08 September 2013 2,430 9 View

I want to know if the binding of drug can actually affect p-p docking?

I mean, (I am not very familiar with protein-protein binding) can a drug accelerate (or oppose) the protein-binding? If yes, then which p-p docking method should I follow (Which have a suitable...

04 May 2013 7,703 1 View

error in running a model in Abaqus

Excessive rotation of nodes in node set ErrNodeExcessRotation-Step1

17 August 2021 0 0 View

error in modelling model in Abaqus

Excessive rotation of nodes in node set ErrNodeExcessRotation-Step1

17 August 2021 0 0 View

MGL tools

20 June 2021 0 0 View

How climate change will influences human and animal behavioral change?

The role of climate change influencing the human behavior as well as economics interest

01 June 2021 0 0 View

flexibility of polymers chain

effect of double bond on the flexibility of polymers

07 April 2021 0 0 View

i have some problem with chtMultiRegionSimpleFoam

--> FOAM FATAL ERROR: Maximum number of iterations exceeded From function Foam::scalar Foam::species::thermo::T(Foam::scalar, Foam::scalar, Foam::scalar, Foam::scalar (Foam::species::thermo::*)(Foam::scalar, Foam::scalar) const, Foam::scalar (Foam::species::thermo::*)(Foam::scalar, Foam::scalar) const, Foam::scalar (Foam::species::thermo::*)(Foam::scalar) const) const [with Thermo = Foam::hConstThermo >; Type = Foam::sensibleEnthalpy; Foam::scalar = double; Foam::species::thermo = Foam::species::thermo >, Foam::sensibleEnthalpy>] in file /home/ubuntu/OpenFOAM/OpenFOAM-4.1/src/thermophysicalModels/specie/lnInclude/thermoI.H at line 66. FOAM aborting #0 Foam::error::printStack(Foam::Ostream&) at ??:? #1 Foam::error::abort() at ??:? #2 Foam::heRhoThermo >, Foam::sensibleEnthalpy> > > >::calculate() at ??:? #3 Foam::heRhoThermo >, Foam::sensibleEnthalpy> > > >::correct() at ??:? #4 ? at ??:? #5 __libc_start_main in "/lib/x86_64-linux-gnu/libc.so.6" #6 ? at ??:?

24 March 2021 0 0 View

Formulation of polymer color flakes

I am writing to request some information for making polymer color flakes. I would appreciate the help.

17 March 2021 0 0 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

What's the best way to measure growth rates in House sparrow chicks from day 2 to day 10?

What's the best way to measure growth rates in House sparrow chicks from day 2 to day 10? Since, the growth curve from day 2 to 10 won't be like the "Logistic curve" it might not follow logistic...

03 March 2021 1,401 3 View

What is the production process of CaFe ferroalloys?

I looking for ferro calcium production process

03 March 2021 1,755 4 View