Tools for modeling 3D structures of complex saccharides?

I want to model some complex polysaccharides containing non-conventional saccharides as building units. The structures should retain the proper glyscosidic linkage. Please suggest me some tools...

08 September 2016 1,270 11 View

How to calculate diffusion rate of a molecule into the solvent using molecular dynamics simulation?

09 October 2015 2,351 1 View

Can we use the potential energy values generated after minimization of small molecules, to compare their stability?

Its well known fact, potential energy generated by molecular minimization usually used to check molecules stability and is the function of torsion energy, bend energy, bond stretch energy,...

05 June 2015 4,676 15 View

What's 'single-trajectory' simulation and how is it different from normal MD simulation?

Which is best for ligand-protein complex, binding affinity calculation?

05 June 2014 3,774 5 View

What is the basic step for doing Proteochemometrics modelling?

.

11 December 2013 1,892 1 View

How to differentiate among the mode of binding of ligands in different proteins having same set of identical or similar active site residues?

I am doing docking studies on some proteins belonging to same protein family but different organism, but don't know how to differentiate out the difference in binding mode of ligands to the...

10 November 2013 5,953 1 View

Could anyone give a suggestion regarding substitute for MD simulation for binding energy calculation of docked protein-ligand complexes?

I have done the docking by using DOCK6 software and on the basis of good poses and grid score sorted out a good docked ligand conformation. Now I want to calculate the accurate or some what close...

10 November 2013 2,902 3 View

Are there any bioinformatics tools which can identify the physicochemical properties of binding pocket of different protein?

I want to identify the physicochemical properties of binding pockets of different proteins, as it has reported in some literature that the binding pocket of each protein has different and unique...

10 November 2013 3,320 9 View

Which should be given more importance docked good poses or binding energies of docked ligands?

.

09 October 2013 8,496 20 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

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

What kind of fluid could I use for a pitfall trap that also does not invalidate molecular testing?

Hi, I want to start testing pitfall trap to obtain ants samples, but I need to conduct molecular analysis on those insects. So, what kind of fluid can I use? Ethanol expires too early and I need...

03 March 2021 5,978 5 View

Arena simulation - how do i model the following model in ARENA (see description) (new to ARENA)?

Hello, I'm fairly new to ARENA and I have the following problem: I have two queues in which, in each queue, a different order type arrives (both having an arrival rate of exponential 10). Order...

02 March 2021 2,431 3 View

Why are the velocities so high in my Boussinesq approximation Fluent simulation?

Hello, I have a mechanism where air rises due to convective flows. In this simulation, nothing is driving the air except this. I understand that the Boussinesq approximation only works for small...

02 March 2021 4,910 3 View

How to repeat an operation on an atom selection for multiple times in PyMol?

Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...

02 March 2021 4,569 4 View