Which force field to use for Protein-DNA interactions in Molecular Dynamics?

More Anthony Nash's questions See All

How to get hydrogen bond analysis using MDAnalysis working with custom atom names?

Hi, I'm up against a horrible deadline so I'm hoping for some help figuring out what I'm doing wrong. I have a list of custom atom names in Gromacs of which I want to perform hydrogen bond...

31 December 2019 8,270 5 View

How to add periodic rendering in PyMol?

I have a licensed copy of PyMol (ver 2.3.1) and I am looking to 'replicate' a protein/bilayer i.e., in VMD you select "Periodic" and select from a number of x, y and z options. This, in turn,...

11 December 2019 7,494 4 View

How to resolve GROMACS mdrun seg fault during minimisation?

I'm waiting on email conformation for the GMX user group, but this is in reply to Reviewers so I'm pressed for time and asking here. I'm building a small collagen-based system. The crystal...

10 November 2019 4,275 8 View

How do derive force constants from QM into MD for drugs and small compounds?

Hi, I know the fundamentals, I'm would like an update on the available open-source software. I have a set of small molecules and drug molecules. I've derived their ground state structure using...

10 November 2019 9,586 3 View

How to increase the number of optimisation steps in ORCA?

What is the keyword to increase the number of optimisation steps (not the number of SCF steps) in an ORCA optimisation calculation? The warning is suggesting I increase the "number of...

08 September 2019 1,843 2 View

Are these QC DFT settings appropriate?

I'm picking up quantum chemistry after a three year break. I've forgot a lot and I'm now using ORCA (version 4.0.1.2). My system is a non-enzymatic chemical reaction between lysine, arginine...

07 August 2019 1,651 3 View

Looking for CHI (transmembrane modelling software)?

I am looking for an old piece of software called CHI. It was used to model protein transmembrane domain interactions in a gas phase. I believe it was part of...

01 February 2019 5,274 2 View

How to change the amino acid in a Gromacs topology and force field file?

Hi all. A similar question to this has been asked several times, however there is subtle difference. I would like to change e.g., an alanine to a glycine (or any amino acid) in a .gro file AND...

11 December 2018 677 11 View

How to calculate whether a disease outcome in a population is by chance or significant?

Hello all, I have a huge dataset of longitudinal medical records. Each record contains indications for drug and disease. I have been able to calculate the Cure Rate in the population given a...

09 October 2018 2,092 5 View

How to determine whether two time-series trajectories are significantly different?

I have six time-series plots as a measurement of some soft-matter physical function F(t), see the graph below. In most instances, it is quite clear that particular variations in the property of...

08 September 2018 418 8 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

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

How to analyze a particular region of my simulation box in GROMACS?

Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...

03 March 2021 9,989 2 View

Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence?

I am on the lookout for the Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence. Does anyone know where I can find it? Thank you in advance

03 March 2021 3,568 1 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

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