Creating workflows in Python. I would like to have your opinions about snakemake?

I would like to know the advantages and the disadvantages of snakemake. Is a there a tutorial with multi-threading options? If you have already used snakemake, it would be useful for me if you can...

11 December 2015 1,625 0 View

Is there an alternative for the python module gzip?

I would like to read directly (in python) gzipped files without extraction. Can someone suggest me an other module than gzip? because currently, gzip takes like AGES before It gives me the output...

03 April 2015 4,150 2 View

What is the role of rhodamine 123 in detecting apoptosis?

Thanks in advance.

10 November 2014 2,526 11 View

Can someone recommend research papers or reviews regarding MMP2, MMP3, MMP9, TIMP1&2?

Interaction between MMP & TIMP

04 May 2014 4,611 6 View

Can we find out the different interactions between proteins; especially between amino acids using bioinformatic tools? How?

What is the best way to find out these interactions? Data analysis or observation or the combinaison of these two?

04 May 2014 5,121 6 View

What is the best way to represent the dynamical structure of a protein?

I have a lot of interaction data between two proteins. But, I don't know what is the best way to analyse and represent these data. By interaction data, I know which aminoacid interact to have a...

04 May 2014 4,435 1 View

Is there a software to get mutated proteins?

I would like to change an aminoacid in a protein sequence. Can someone suggest me a software? Can I change the sequence directly in the pdb file? If yes, how?

04 May 2014 6,818 8 View

Can I use the software named AUTODOCK for protein docking?

Please suggest me other softwares if you know.

04 May 2014 350 8 View

Which is the best software to align sequence?

It can be a DNA sequence, protein sequence.

04 May 2014 7,268 6 View

What is the use of potential energy distribution (PED) that can be got by the software CHARMM and how can it be exploited?

Use of the software charmm.

04 May 2014 444 3 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