How to measure bacterial fitness for modelling evolution?

Hi, I would like to measure the fitness of bacterial species carrying antibiotic resistance genes (two genes in total) and model the evolution and spread of these two strains (with two different...

06 July 2018 6,839 2 View

What force field should I select for protein - ligand complex?

Hi, I am planning to study the mechanism of drug efflux membrane protein using MD simulations. I have successfully docked the ligand. Now I would like to perform MD simulations on the protein....

02 March 2018 5,268 3 View

Are there any web-based MD simulation softwares? Can I use web-based MD simulation software for publishing my results?

Hi, I would like to run MD simulation of a membrane protein using GROMACS or NAMD. However, my institute does-not have high configuration systems, and I have no financial support for purchasing...

31 December 2017 7,337 7 View

Which processor is better for running MD simulations - i7 7700 or AMD Ryzen 1700X?

Hi all, I wish to purchase an assembled PC for running MD simulations myself. My specifications are: 8GB RAM, 1 TB ROM, NVIDIA M2000 GPU apart from all other general features. I was unable to...

10 November 2017 1,578 7 View

How to find gi identifier in BLASTp for submitting y model to PMDB? Any databases other than PMDB for submitting modelled proteins?

Dear all, I have modelled a drug efflux protein using ITASSER. I would like to upload the model in Protein Model Database (http://www.biocomputing.it/PMDB). The accession number is...

09 October 2017 1,829 3 View

How to define parameters for running a MD simulation?

I have been working on understanding the mechanism of efflux mediated drug resistance in bacteria. I was able to successfully model the protein using homology modelling and threading. Now I would...

07 August 2017 6,940 8 View

Generating random numbers for biological research

Hi..I would like to apply random sampling technique for the distribution of genes in a collection of bacterial samples. I would like to test finally 250 samples out of 500. Please suggest me a...

03 April 2017 5,354 3 View

How to choose the method of phylogenetic tree construction?

31 December 2016 6,137 5 View

How to perform in silico analysis of an enzyme's action on gram positive cell wall?

Hi, I wish to apply in silico methods for analysing the activity of a protein. the protein is actually an enzyme that destroys gram positive cell walls. I wish to model the effect of various...

11 December 2016 6,802 1 View

Computational method for calculating enzyme activity?

08 September 2016 4,123 6 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