Does anyone have recommendations for the modeling of compound-compound interactions?

HelloI want to model interaction between C60 and few some chemical compounds in a box with water. Can anybody suggest me any software tool (except gromacs) for such kind of work ? I would be very...

07 August 2015 7,417 5 View

How can I fix the ligand in acpype?

10 November 2014 6,484 1 View

How can I fix the protein in gromacs ?

Hello all Now, I normally can do protein-ligand md in gromacs. But in few cases when I did command: pdb2gmx -ff amber99sb -f ProteinAmber.pdb -o Protein2.pdb -p Protein.top -water spce -ignh I got...

10 November 2014 7,008 13 View

How to correct the number of coordinates in gromacs (grompp).

Hello all I have to do Protein - Ligand MD simulation.Thus I am doing tutorialfor Protein - Ligand...

09 October 2014 1,680 12 View

Can anyone help with biology testing?

I've worked for more than one year on the calculation part of my phd work. The theme of my work is ''Searching of low molecular ligands for SH2 domains". I've already finished the whole...

03 April 2014 5,106 1 View

Can anyone suggest free software for generating all possible isomers and tautomers?

I need make all possible isomers and tautomers for a chemical library (about 10 000 compounds). But, I have never done such work. That is why, I don't know which software package is better to use.

11 December 2013 8,219 22 View

Does anybody know a technique for analyzing chemical databases?

I created a big chemical database (using flexible docking, pharmacophore modeling methods) of potentially active compounds. Now I have a library involving 10,000 compounds. I want to recognize...

10 November 2013 7,998 4 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