How to analyze data set of 53 micro rna genes in plants through SVM ?

I am working on long and short noncoding rnas in plants. I have a dataset of 53 microRNA genes in plants. Please suggest me how to analyse these micro rna genes through SVM technique. Please guide me.

01 February 2016 2,154 2 View

How can I build secondary structure in case of plants?

hello guys. I am working on noncoding rna (short & long both). which method is better to build secondary structure of ncRNA? what criteria should be taken for precursor sequence up &...

10 November 2015 4,199 1 View

Can we modify the result of LigBuilder?

We used LigBuilder, but in our results the molecules don't have their valency fully filled. Can we modify the result which have molecules that do not have full-filled valence parameter or should...

04 May 2014 4,678 0 View

Need help with pdb2gmx command in GROMACS

I am trying pdb2gmx command for MD simulation. but the output of pdb2gmx is not working properly in-case of multiple chains. the output file of pdb2gmx >>> .pdb or .gro was not generated. ERROR...

10 November 2013 8,584 5 View

Problem with pdb2gmx command in Gromacs?

I am working on molecular dynamics simulation in Gromacs. The output of the pdb2gmx is not working properly: only the .itp file and the .top file generate, not the .pdb/.gro files (output files).

09 October 2013 2,011 4 View

How do I compute the ligand binding site through PASS software?

Can anyone provide the full procedure for ligand binding site through PASS software?

07 August 2013 8,977 1 View

What is the base of CL- Ions in GROMACS?

I have a confusion for CL- ions in genion command.

06 July 2013 3,646 3 View

Which parameter is used with grompp>genion command in Energy Minimization in GROMACS?

I found another error through grompp_genion command: command used: grompp_d -f em -c 1chl-b4em.gro -p 1chl.top -o 1chl-4em-1.gro > grompp_b4em_agenion.output ERROR: Program grompp_d, VERSION...

06 July 2013 7,318 1 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