How to refine a protein-drug complex structure coordinates?

More Francisco J. Enguita's questions See All

Do you have a template for miRNA qPCR arrays from Qiagen (former Exiqon)?

Dear colleagues After a lot of struggle with the new rebranding of Exiqon that sold the LNA technology to Qiagen, we decided to give a try to the new miRNA qPCR arrays. We bought the whole...

11 December 2019 7,009 3 View

RNAse R... which supplier?

Dear All I am looking forward to treat my total RNA samples with RNAse R. Any suggestions about which supplier do you prefer for purchasing it?. Thanks. Best

09 October 2018 9,378 5 View

How to over-express a selected circular RNA?

Dear All Do you have experience in methods for the over-expression of selected circular RNAs in human or mouse cells?... If yes... which strategy did you use?... which vectors and...

06 July 2018 7,523 1 View

What is your favourite Gene-enrichment analysis in a graphical environment?

Hi there I would like to know and to get your feedback about you favourite Gene-enrichment analysis software based in a graphical environment, preferably on-line. Please give me your feedback...

05 June 2018 8,910 9 View

How is the performance of Nanostring system to detect extracellular miRNAs?

Dear All I wanted to give a try to Nanostring system to detect extracellular miRNAs in a screening-based approach. I am wondering if some of you have experience with Nanostring in the detection...

05 June 2018 7,494 3 View

Someone has experience with the new Exiqon-Qiagen miRNAnome qPCR screening panels?

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How to compare two XPM contact matrices generated by GROMACS?

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11 December 2017 8,805 12 View

Any web-based tool to get statistics about location and miRNA expression?

Hi there I am dealing with a long list of miRNAs... I would like to get some tool to organize them by functional groups, clusters, chromosome location, tissue expression, etc... Any suggestion?....

09 October 2017 8,407 4 View

Is there any alternative to Green A Dyematrex gel (Amicon) for pseudo-affinity chromatography?

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08 September 2016 1,844 3 View

Any tool for the analysis of coarse-grained MD trajectories with NAMD?

Dear All I have several MD trajectories generated by NAMD using coarse-grained dynamics. I would like to perform a deep analysis of the data. Is there any specific tool for this kind of...

01 February 2016 4,771 7 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

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

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

Ramin Ekhteiari Salmas

A short MD simulation can be a good option to relax the binding domain.

You may continue the simulation until to get a stable RMSD values for the ligand (drug).

It depends to what you mean from equilibration - if your system is not in a good mood (has higher total energy or some overlapped atoms or it's embedded inside a membrane atoms) it's better to equilibrate it by a short minimization or a short simulation with some harmonic constraints if it needs.