How do cancer cells grow without tumor microenvironment?

In the body, when one develops a tumor, the microenvironment is very important. How do the cell cultures of cancer cells grow in the flasks without that micro-environment and only with the media...

01 February 2020 2,853 4 View

How to desalt zwitterions?

I am trying to synthesize a compound which has both carboxylic acid and amine. During the purification, when I do the pH adjustment it forms a zwitterion and goes into the aqueous layer. Is there...

01 February 2020 6,594 3 View

What are the alternatives for FBS in cell culturing?

I am trying to grow cancer cells and do MTT assay for drug screening. Are there any alternatives to FBS? I know that FBS and FCS are widely used for cell culturing, but I am looking for other...

31 December 2019 4,663 4 View

How does protonation of aminoacids in cellular environment occur?

Some proteins change their conformation based on protonation state of particular residues like aspartic acid. Some kinases are examples for this. For example, in case of Abl kinase, protonated...

10 November 2019 5,279 5 View

Will running very long molecular dynamics cross the energy barriers and explore different conformations?

I am working on computationally understanding the active and inactive conformations of some proteins. Simulating the inactive conformation from the active conformation is reported in literature by...

09 October 2019 5,721 3 View

How to analyze the van der waal's interactions of a residue through a simulation?

Is there a way to quantify (eg.: plots) the van der waal's or other hydrophobic interactions of a residue through a simulation? For example, using VMD, we can check for salt-bridges and hydrogen...

07 August 2019 668 3 View

Any TLC stain to detect presence of boron/boronic acid?

I am trying to synthesize boronic acid pinacol ester derivatives from aryl/hetero-aryl halides. Is there any TLC staining technique which can indicate the formation of boronic acid? Thanks.

03 April 2019 323 10 View

Are there any bioisosteres of triple bond?

Are there any bioisosteric replacements of triple bond (alkyne) which were employed for lead optimization or scaffold hopping? Thanks.

03 April 2019 2,601 5 View

Is HATU((1-[Bis(dimethylamino)methylene]-1H-1,2,3-triazolo[4,5-b]pyridinium 3-oxid hexafluorophosphate)) stable upon heating?

I am doing an amide coupling reaction using HATU. The starting material is not very soluble in DMF. So, I am thinking of heating the reaction mixture to 65C. Is HATU stable at that temperature or...

08 September 2018 3,392 3 View

What is a collective variable in metadynamics?

I am trying to do metadynamics simulation for my protein. Can someone explain what is a collective variable, and on what basis we decide collective variables in a metadynamics run? Thanks.

07 August 2018 5,555 4 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

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

MGL tools

20 June 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

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

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

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

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