How can I install ProDy?

I want to do normal mode analysis through ProDy i am not able to install on window platform please provide me step bu step method to install ProDy. I have tried website method it is not working in...

03 April 2016 9,608 5 View

Can anyone help with molecular dynamics of amyloid fibril?

I am doing MD of amyloid fibril pdb in 2BEG with gromos 56 force filled for 20 ns. When I visualize in pymol in my simulation after 15 ns one or two chain dissociate from the protein and come...

01 February 2014 7,625 4 View

Any advice for the simultaneous simulation of multiple ligands?

I have used blind docking (as binding site is not clear) approach to my target protein and finally I have clustered the poses. We have a ligand bind to 3 probable binding sites and have already...

31 December 2013 876 3 View

I am not able to understand this comment about docking - can anyone help?

The description of the docking results was limited. They showed results for only one docked pose for each of the four compounds. What was the basis for selecting this one pose? Often single poses...

11 December 2013 5,654 2 View

Workstation recommendations.

I want to buy a workstation for bio molecules simulation for minimum of 100ns. Can any one suggest the best configuration? xenon E5 1650, 3.02 Ghz,12 Mb cache, 12 GB of Sata RAM, DDR3, NVIDA...

03 April 2013 5,561 4 View

What will be the correct Descriptor for 2D QSAR 3D QSAR. How to use Genetic Function Approximation in selecting descriptor?

2d qsar 3d qsar.

02 March 2013 4,049 7 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