Does gromacs 5.1.2 input files compatible with mdrun with Gromacs 4.5.6?

The Gromacs 5.1.2 installation on my Ubuntu 16.04 works perfectly fine for mdrun with Protein-Ligand complex using CHARMM ff. Now, I want to carryout mdrun on a external server where Gromacs 4.5.6...

06 July 2018 4,097 5 View

How to find measure ligand-ligand interactions?

Dear all, I want to study the interaction between one organic molecule with other. The hypothesis is some of the key interaction like hydrogen bond formation or lattice energy involved or ethalpy...

09 October 2016 7,951 3 View

How can we carry out energy minimization of protein?

If the protein structure available is not full and only catalytic site residues with co-crystallized ligand with highest resolution (1-2 A0) is available. I want to know how the energy...

07 August 2014 1,192 3 View

Is anyone familiar with using PLS_Toolbox from eigenvector in MATLAB?

I want to know about PLS regression. QSAR model is built with PLS regression with 100 descriptors using LOO cross validation and 4 latent variables. I want to know the contributions of each...

04 May 2014 8,389 6 View

Topology from mol2 file

I want to generate a top file for a MD simulation in Gromacs. I specifically want all atom topology. The ATB server indeed generated such topology, but I want to use Amber charges loaded in mol2...

02 March 2014 443 10 View

Is it possible to have a pyrimidine derivative from mannich product (beta keto amine) by condensation with urea with a suitable catalyst?

Can anyone tell me whether a pyrimidine derivative is possible from mannich product (beta keto amine) by condensation with urea with suitable catalyst? I have synthesized 2,4,6 tri substituted...

01 February 2014 2,497 4 View

Energy minimization?

Gaussian 03 can perform energy minimization by applying various basis sets like DFT/B3LYP level 19 and using the cc-pVDZ. Which other free software can carry out similar types of optimization?

31 December 2013 9,117 15 View

Is anyone familiar with the reaction of 1,3-benzodioxole, derivative of 7,8-dihydroxy coumarin?

I have tried the 2-substituted 1,3-benzodioxole derivative of daphnetin (7,8-dihydroxycoumarin) by literature methods of 2-substituted 1,3-benzodioxoles of catechol and aromatic acids. I have...

09 October 2013 3,717 1 View

Organic Chem problem

Hi, all there!!! I want to know how to calculate the molar ratios to be taken in the multicomponent reaction?

06 July 2010 5,472 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