Juan Carlos Muñoz García

7 Questions 6 Answers 0 Followers

Questions related from Juan Carlos Muñoz García

I have built a cellulose fibril model using Cellulose Builder (http://cces-sw.iqm.unicamp.br/cces/). How can I oxidised the surface (C6 oxidation)?

I trying to find the best way to introduce a COO- group at position 6 for some of residues at the surface of my cellulose fibril, either randomly or following a pattern.

08 August 2017 1,603 0 View

Do you know a good/fast tool to analyse protein-lipid interactions from a MD trajectory (GROMACS trajectory)?

I mean the number of contacts per protein residue with different different parts of the lipids. It more or less can be done in GROMACS, but you need to create many indexes for each trajectory, so...

11 November 2014 168 1 View

Problem inserting protein into a POPC bilayer?

I’m trying to embed a GPCR-ligand complex into a 128-lipid POPC bilayer (popc128a.pdb structure from Peter Tieleman’s group) using the following set of commands with GROMACS 4.6.5 (of course the...

05 May 2014 4,918 5 View

Why do constraints equal all-bonds during production run?

I’m quite new with GROMACS. I come from using AMBER for a long time and after doing quite a few GROMACS tutorials I’ve found in all of them that the variable “constraints" is set to “all-bonds”...

04 April 2014 3,387 5 View

How can I do ensemble docking with Autodock Vina?

I want to do ensemble docking using different conformations of the receptor from MD with Autodock Vina? Is there any script available for such thing?

04 April 2014 770 3 View

Have you ever had problems when loading .trr and/or .trj GROMACS trajectory files in VMD?

I'm a new GROMCS user. I've run an NVT equilibration of a explicitly solvated protein-ligand complex, I've extracted frames throughout the trajectory in both .pdb and .gro format and I've open...

03 March 2014 8,253 1 View

Is there any software or script to transform a coarse grained pdb file to atomistic without knowing the definition of the beads used in CG?

I've tried CG builder of VMD but it does not work

01 January 2014 4,368 2 View