Please anyone to help in preparing qm/mm input files by "namd" (Molecular Dynamics software) for a ligand-enzyme complex?

Hi All, I'm trying to prepare qm/mm files for a ligand bound to an enzyme, I followed the tutorial of "vmd" and "namd", but it still reports an error in qm calculations. Any idea please? Best,

08 September 2018 808 0 View

Can anyone please help in finding the Fourier transform of the distance equation?

Can anyone please help in finding the Fourier transform of the distance equation? The distance equation is: (Z2-Z1)2+(Y2-Y1)2+(X2-X1)2=D2 X1,Y1,Z1 are the coordinates of the first point. X2,Y2,Z2...

04 May 2017 131 3 View

I need simple executable to perform steepest descent minimization for protein structure (pdb)?

Hi all, I need simple executable to perform steepest descent minimization for protein structure (pdb), with instruction how to do it? Thanks,

10 November 2016 7,700 1 View

How to Call NAMD Molecular dynamics software from *.bat file on windows?

09 October 2016 7,401 0 View

How I can apply random incremental pulse search (RIPS)?

Hi All, Can any one please tell me how I can apply "random incremental pulse search" (RIPS) for side chains of amino acids interacting with certain ligand. Which software (with link to the...

08 September 2016 1,726 0 View

Where can I find forcefields for phosphoserine to use with "NAMD"?

05 June 2015 7,007 6 View

With NAMD, where can we find standard config files for minimization, heating, equilibration,and production for all types of ensembles (NVE,NVT,& NPT)?

With NAMD, Where can we find standard config files for minimization, heating, equilibration, and production for all types of ensembles (NVE,NVT,& NPT)?

02 March 2015 6,106 4 View

In Molecular dynamics, which ensemble is better to use: NVE or NVT?

We use different ensembles in MD, which one is preferred to use?

02 March 2015 7,295 14 View

How can we solve the problem of energy drift in NVE ensemble in Molecular Dynamics?

How can we solve energy drift problem in NVE (constant energy, constant volume, and constant number of particles) ensemble in Molecular Dynamics?

02 March 2015 1,207 3 View

In Molecular dynamics (NVE), is energy drift of about +5 Kcal/mol.ns acceptable?

In Molecular dynamics (NVE ensemble), is energy drift of about +5 Kcal/mol.ns acceptable?

02 March 2015 3,680 2 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