How to determine protein stability using GROMACS?

31 December 2016 7,476 18 View

What is importance of OXT atom found in aspartic acid? Does it participate in salt bridge formation?

During a molecular dynamics simulation i have found salt bridges being format being N(eta) atoms of Arg and OXT atom of Asp. What is the role of OXT atom and is such a salt bridge formation possible?

08 September 2016 10,030 3 View

Calcium as a chaotrope or kosmotrope?

04 May 2016 4,266 4 View

What is meant by molecular or rotational tumbling of proteins?

Several computational models describe rotational tumbling and rotational relaxation time when describing protein motion and dynamics. What is meant by relaxation time and how is related tumbling?...

09 October 2015 4,119 5 View

Which is a more appropriate forcefield ff99IDP (AMBER) or OPLS for disordered proteins?

I wish to observe disorder-order transitions using MD. Which would be a more appropriate and accurate forcefield, ff99IDP (AMBER) or OPLS?

06 July 2015 3,387 4 View

What is the ideal time frame for molecular dynamics simulations?

I wish to observe helix-coil transformation using MD simulation. What would be the minimum time scale for the simulation to observe such conformational transitions?

06 July 2015 7,532 3 View

Is there a way to study peripatric speciation using bioinformatic approach?

10 November 2014 2,269 1 View

How can I study the evolution of disordered proteins?

Is there as way or approach to understand and study the evolution of intrinsically disordered proteins based on their amino acid sequences using phylogenetics?

09 October 2014 1,617 3 View

What is the importance of glutamine in a protein's structure and function?

I have noticed that several microtubule-associated proteins contain stretches of glutamine residues. Is there a particular reason for the presence of such Q-rich regions?

09 October 2014 8,815 5 View

How did neurons evolve?

neurons are largely made of a cell body, dendrites and the axon. How did the neuron evolve into such a complex structure? Was the first neuron only a cell body and later developed axon and dendrites?

09 October 2014 7,120 0 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