WHy the docked substrate move out from the active site of the protein during MD simulation?

I have docked the substrate in the active site of the protein ( contains NAD and lactate substrate ), interacting with binding residues through hydrogen bonding. When i start the MD simulation...

31 December 2018 6,931 11 View

How to correct the number of coordinates in gromacs file (solv.gro, topol.top)

Respected All, I am going to do the Ligand MD simulation using Justin Lemkul tutorial (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/03_solvate.html). After...

31 December 2016 156 4 View

Which statistical test is appropriate for unequal sample size with less mean difference?

I have worked on vocal behavior of rats during a diseased condition and found 8 different type of calls but of unequal size with less difference among means in their temporal parameters despite...

05 June 2016 8,770 3 View

How to calculate Surface electrostatic potential using pymol?

Hi all, please can any guide me on easy way to calculate Surface electrostatic potential of a protein using pymol? or there is any free online server?

31 December 2015 3,022 2 View

What is the relatioship between the potentail energy and protein structure?

I have modeled a wild protein structure and their five mutant structure. Now i have analyzed their potential energy for normal and mutants. Potential energy calculated for wild, Pro420Arg,...

31 December 2015 8,947 10 View

How to find the sequences responsible for the aerobic nature of the enzyme through phylogenitic analysis?

Hello, I have amino acid sequences of the same enzyme in more than 150 different organism which is grouped in two form i.e Aerobic and anaerobic enzyme. I did blasting of these sequences but i...

01 January 1970 266 1 View

How to merge two subunit of protein through linker by homolgy modeling?

Hello, I have two subunits (let say alpha and beta) between them a linker sequence (29 amino acid). I have modeled the alpha and beta subunit using templates extracted from PDB. There is no...

01 January 1970 2,872 12 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