What can molecular dynamics say about protein-ligand interactions?

Can it say anything about changes in domains if the protein ligand interacts with only one domain?

31 December 2012 6,485 5 View

Can anyone suggest some good standalone programs with interactive 3d structure alignment and motif search?

I need to do structure alignment on 2 isomeric protein and two homologous protein. Any suggestions?

10 November 2012 3,018 4 View

Has anyone used Autodock vina pymol plugin?

I want a detailed tutorial

08 September 2012 696 1 View

How are cells able to survive at -80 degree Celsius as all the water (80% of total volume) will freeze and volume will increase leading to lysis?

I want to know how cells can remain active after so many years at -80 or even lower temperatures. I understand that enzymes would renature after thawing but still what is the molecular mechanism?

07 August 2012 8,982 22 View

Is there any open source chemical file format converter with batch conversion module other than open babel?

I am looking for a converter which can convert 50-60 molecules from .mol2 to .mol format in one go.

07 August 2012 3,247 7 View

When using autoclave we use autoclave tape which changes color to black indicating autoclaving was successful, what is the molecular mechanism?

Why do we use tape as an indicator?

07 August 2012 8,849 5 View

What are tools available to check the accuracy of model protein structure?

I wish to know the details on how to rate the structure modeled using modeller.

07 August 2012 1,372 21 View

Protein structure prediction

With hundreds of tools for the protein structure prediction from primary sequence, can anyone provide a logical approach for higher accuracy? While there are many methods for homology based...

07 August 2012 6,938 3 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