Call for Book Chapter: Essentials of Bioinformatics Vol. I-III (Springer) (Last Date Extended to 15th of Nov) ?

09 October 2017 8,712 0 View

Call for Book Chapter: Essentials of Bioinformatics Vol. I-III ?

08 September 2017 6,664 0 View

How to use the "qsub" command to run the MD simulation (Gromacs) job in Servers

I am using a server to run MD simulation of my protein. According to instruction of the server it is showing that "Use qsub to run your jobs else your jobs will be automatically killed after...

09 October 2013 6,670 4 View

I had a protein model with more than 2000 amino acids; when I performed protein-protein docking with these proteins I am getting "0" energy values.

I had used different protein-protein tools like Hex, patch dock, zdock, prodock etc., all are showing similar kind of +ve energies, but when I cut model into two different chains they are showing...

03 April 2013 8,303 4 View

I built a two chain of my protein model, now I need to build this model as a single protein model, what tools do I need to use to perform this?

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03 April 2013 6,422 7 View

I want to build a protein structure which contains more than 2000 amino acids?

I had a protein which contains more than 2000 amino acid in length, unfortunately the blastp results didn't show any identical templates and even the ab-intio server (robetta and itasser) cut off...

02 March 2013 8,081 8 View

How do I perform Protein-Protein docking?

I had a homology model protein, that I needed to dock with solved protein structure (which is inhibitor of the build model). The crystallography structure consist of homologus hexamer in its...

02 March 2013 7,077 9 View

What database do I need to search the homologous sequence in the identified bacterial sequence?

I had a 16s bacterial sequence, for identification of its similar sequence in blastn what database do I need to choose (either I need to choose nr/nt database or 16s ribosomal RNA sequence).

01 February 2013 211 9 View

After getting the 16s rDNA bacterial sequence, how much identity is required to submit to the National Center for Biotechnology Information (NCBI)?

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01 February 2013 5,464 2 View

Looking for a protocol for complex DNA-Protein Dynamics (gromacs).

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01 February 2013 8,895 9 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