Does anyone know why am I getting the error using HADDOCK 2.2 web server?

I am trying to dock two proteins using HADDOCK web server (prediction interface). I have done the changes reres, delocc... but I still having the error message: First pdb file contains multiple...

01 February 2017 2,971 3 View

Is possible to simulate a trimer using gromacs package?

10 November 2014 9,318 6 View

Can anyone help with FEL (Free energy landscape)?

I have computed a representation of the free energy landscape (FEL) sampled by my trajectories of MD following the tutorial as attaching . I would like to know if there is one specific reason as...

06 July 2014 5,827 2 View

What is the meaning of a density graphic?

What is the meaning of a density graphic generated with data from a molecular dynamics simulation (was used the GROMACS and the Gromos force field)?

06 July 2014 8,435 3 View

Can anyone help with using -fit rot+trans?

I tried to fit the whole trajectory from molecular dynamics simulation (using Gromacs) using the initial structure (using -fit rot + trans), but when I compare two structures they are not aligned....

05 June 2014 6,564 8 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

How to get onecolumn document from standard IEEE ACCESS LateX template?

I have prepared a manuscript in IEEE Latex template, but for some purpose, I need to prepare a word file as well (detailed format is not required). Compared to two column .tex file, one column...

02 March 2021 1,830 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

Why Austenite grains in steel show much more twinning than ferrite grains?

It is oftentimes said to be a distinctive metallographic trait that differentiates a fully austenitic and a fully felly ferritic steel without etching that might distinguish between two. Why...

02 March 2021 728 2 View

How can the modification of garden soil cause global warming?

Hello, I am working on a soil project and I found a primary research article that tests how the modification of agricultural soil can cause global warming, using a thermal collector, however I...

02 March 2021 7,161 3 View

Does anyone know how to plot my station to a section plot on Ocean Data View (ODV)?

I made a vertical section plot with WOA .nc file on ODV, and now I want to plot my stations (csv. file) in it. Does anyone know how to import my points to the section? They are two different...

01 March 2021 3,610 1 View

Why might my GFP tag be dissociating from my plasmid after transfection?

I have a set of stably transfected cell lines all transfected with plasmids containing GFP tags on the C terminus. During a western blot using anti-GFP antibody, one of my plasmids has dissociated...

01 March 2021 9,310 4 View

Does anyone know to clarify these changes?

01 March 2021 1,290 2 View

Precipitate after adding laemmli buffer to protein solution containing Potassium Acetate?

Hi, I am running a size exclusion chromatography experiment with a buffer containing Potassium Acetate as a salt. I analyse these fractions through SDS-PAGE. After boiling my SEC fractions in...

01 March 2021 2,622 3 View

What is the most suitable server for predicting protein structures in bacteria?

I have used the i-Tasser several times, however it has been unavailable for several days. I tried the swiss-model, but the output was not very pleasant due to the model used. Is there any other...

28 February 2021 4,521 3 View