How can I calculate PCA for a particular domain of a protein simulated using Gromacs?

I simulated a 600 a.a receptor containing two separate 300 a.a domains in complex with three different ligands. I want to calculate and compare the collective motion of each domain in these three...

09 August 2020 6,074 2 View

Is Amber03 a reasonable force field to simulate protein structures and dynamics?

I performed a molecular dynamics simulation for a peptide-receptor complex using the Amber03 forcefield and TIP3 water model. The simulation is convergent in 50ns. Based on the Amber tutorial,...

05 April 2020 3,985 4 View

S1142 primer sequence ?

does anyone know about S1142,S142 OR S1461 primer (Sangon products) ? I want the sequence..

16 August 2018 7,775 1 View

I want to run RAPD test for CHO identification,could anyone suggest some good RAPD primer please?

i want to run RAPD test for CHO identification ,could anyone suggest some good RAPD primer please? and does RAPD is a way to differentiate intra species differnces?

16 July 2018 9,460 2 View

How can I set the pressure in NPT phase of molecular dynamic simulation?

We could set temperature with kinetic energy in MD. How about pressure in NPT phase?

19 January 2015 8,805 7 View

How should I treat the peptide with the cells?

The following is written in the article below: (A) Cancer cells in 6-well plates were treated with mouse pept ( 2 mM), human peptide (4 mM) or control peptide (4 mM) in a medium containing 2% FBS...

28 June 2014 8,278 6 View

Can anyone help regarding insulin as a growth supplement for culturing HS578T cell line?

I don't have access to bovine insulin which used add the protocol of cell culture. I want to use human insulin for the culture so I have three question: first, has anyone used human insulin for...

25 May 2014 4,596 5 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

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

Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence?

I am on the lookout for the Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence. Does anyone know where I can find it? Thank you in advance

03 March 2021 3,568 1 View

Resistor definition in Piezoelectric bimorph with ANSYS workbench

Hello, good day! I am trying to simulate similar bimorph piezoelectric harvester with below commands. However, the output power doesn't change with resistor value. Please help to find the reason. ET,10,CIRCU94,0 !SET UP RESISTOR R,1,100000 !RESISTANCE VALUE TYPE,10 !SET ELEMENT TYPE E,1,2 !CREATE RESISTOR BETWEEN NODES 1 AND 2 Thanks in advance Regards,

02 March 2021 0 0 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

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

Why might my GFP tag be dissociating from my plasmid after transfection?

I have a set of stably transfected cell lines all transfected with plasmids containing GFP tags on the C terminus. During a western blot using anti-GFP antibody, one of my plasmids has dissociated...

01 March 2021 9,310 4 View

Why does two different bioinformatics tools for the same proteins show different subcellular localizations?

During a computational analysis, I found that for a protein of a plant, two different subcellular localizations are seen using CELLO and WoLF PSORT. For example, in CELLO, it identified the...

01 March 2021 6,729 2 View