Xabier Arias

6 Questions 17 Answers 0 Followers

Questions related from Xabier Arias

How to perform a MD simulation of a protein with post-translational modifications in Gromacs?

Hi all, I am planing to perform a MD simulation of a protein with two acetylated lysines. Which workflow do you recommend me to follow? Has anyone used Vienna-PTM 2.0? any preferred force...

07 July 2019 8,599 2 View

Is it possible to modify a .tpr file in Gromacs (delete the solvent and ion molecules)?

Hi all, I am trying to make a movie from a MD simulation using Chimera 1.12. This time I am facing problems because the .xtc file is too large (above Gb) and my computer freezes. If I use a...

03 March 2019 7,802 3 View

How should I perform a MD simulation of a glycosylated protein in complex with GSH (reduced Glutathione) using Gromacs?

I am planing to perform a MD simulation of a glycosylated protein (550 amino acid long protein with 6 NAG residues ) in complex with GSH using GROMACS. I wonder if I can ignore these sugars in...

05 May 2018 1,383 3 View

Is passage number important in well-established secondary cell lines?

For the first time I'm gonna start culturing some eukaryotic cell lines and the passage thing is confusing me a little bit... in the case of well-established secondary cell lines (Hela, MCF7 or...

12 December 2017 1,424 4 View

sample precipitation after long PCR

Hi Guys, I´ve been performing a long PCR determination of coagulation factor VIII intron 22 inversion (with SequalPrep kit from invitrogen (A10498)). In the beginning everything was fine and I...

03 March 2011 5,596 5 View

Gromacs: Calculation of an average NMR ensemble structure

Hi guys, I want to perform some MD simulations of a protein that has been resolved by NMR spectroscopy (thus it has multiple structure models). Should I start with an average structure or should...

01 January 1970 1,488 5 View