Is there any available Protein-Protein Docking MD simulation protocol by Gromacs software ?

I have protein protein docking complexes of some vaccine, i would like to perform MD simulation Studies of complexes using Gromacs software, Please help if anyone have standard protocol or...

06 July 2019 6,361 4 View

How to implement chemical structure similarity search tool in local website?

Hello all, I want to embedded a chemical structure similarity search tool in my website (Database), but i was unable to do so, I know that Marvin do provide such facilities but I want some...

03 April 2018 9,431 3 View

How to identify the Pseudogene in whole genome sequence ?

I have to identify the number of pseudo gene present in genome sequence, Please suggest me what are the methods by which i can identify the pseudogene sequences. Please suggest me some...

05 June 2017 6,777 3 View

How to identify the pseudo gene by insilico method from genome?

i have to identify the number of pseudo gene present in genome, what are the methods by which i can predict and identify these pseudo sequences. Please suggest me any online or offline tool or...

03 April 2017 6,980 3 View

Is there any method to retrieve the full length protein sequence from denovo sequenced draft genome data?

By using Augustus gene predictor i have predicted the genes from draft genome but, how should i confirm that these proteins were full length or incomplete? is there any bioinformatics approach to...

04 May 2016 2,955 2 View

Removing specific multiple lines from a text file using perl - any thoughts?

I have file with 6000 line from these some are not useful i want to remove those lines by using perl program. Say input file...

03 April 2014 2,246 5 View

Can anyone tell me how to convert Fasta format (.fasta) multiple sequences into (.nhx OR nh) format for phylogenetic predictions?

I want to generate phylogenetic tree of my protein sequences by TreeBest software for that I want my sequences in these format (.nhx , .nh or .mfa ) for further analysis right now they are in...

31 December 2013 5,755 7 View

Can anyone suggest any tools or software for protein-protein interactions?

specially for host-pathogen PPIs.

09 October 2013 7,513 5 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