Nubia Prates

6 Questions 16 Answers 0 Followers

Questions related from Nubia Prates

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...

02 February 2017 3,006 3 View

Is possible to simulate a trimer using gromacs package?

Dear Gromacs users, I would like to know if is possible to simulate a trimer using gromacs package?

11 November 2014 9,352 6 View

How do you represent the three subunits of a trimer using VMD, PyMOL or Chimera?

I have a protein pdb file (only one subunit), but I want to represent it in the form of a trimer (as attached).

07 July 2014 3,297 3 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)?

07 July 2014 8,474 3 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...

07 July 2014 5,871 2 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....

06 June 2014 6,618 8 View