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?

More Juan Carlos Muñoz García's questions See All

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.

07 August 2017 1,599 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...

10 November 2014 165 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...

04 May 2014 4,916 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?

03 April 2014 768 3 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”...

03 April 2014 3,383 5 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...

02 March 2014 8,251 1 View

Are there instances where molecules with larger molecular weights exhibit greater mobility than those with smaller molecular weights?

Hi, I know that low molecular weight (MW) molecules generally tend to have higher mobility, while high molecular weight molecules tend to have lower mobility. However, in my experimental...

06 August 2024 1,495 2 View

For an in-vitro drug release study, what molecular weight cut-off (MWCO) dialysis bag is required for a 117 kDa protein?

kindly reply me. Thanking you in advance.

05 August 2024 7,727 4 View

How to Add Missing Water Molecules in Protein-Membrane Simulations?

I have protein-membrane simulations (PDB, PSF, DCD) and have noticed that water molecules near the protein are not visible in the simulations. How can I fix this issue? Is there a way to place the...

04 August 2024 1,200 2 View

How to start a Molecular Dynamics Simulation?

Is it possible to conduct a molecular dynamics simulation to see the effects of a specific carbohydrate on the structure of lipids (e.g., micelle structure)? I am a beginner in this field and plan...

03 August 2024 3,371 3 View

Which will be the best software for the Hydration shell analysis with molecular dynamics?

I am using a windows system, what software I should use for hydration shell analysis with molecular dynamics?

02 August 2024 3,143 4 View

Can anyone provide me with molecular docking softwares/ websites?

Molecular docking software/ websites?

02 August 2024 8,704 7 View

CAD File of human's & rat's respiratory airways ?

Dear all, I am working on particle deposition in human's & rat's respiratory airways using CFD and I am looking for the 3D CAD file for my simulations (STEP or IGES format). If somone has such...

29 July 2024 1,092 2 View

How to restart MD without using checkpint file in GROMACS?

Dear All Gromacs User I would like to restart MD without using checkpint .cpt files? I heard there is a way for acheiveing this. Any input and sugegstions are most welcome. Thanking You Budheswar

29 July 2024 3,084 8 View

AutoGrid and Autodock 4.2.6 window opens for 1 second then closes and there is no output files?

Good day, I am a student trying to work on Autodock for a project regarding Ligand-DNA interaction so i am quite new to molecular docking. i have followed tutorials and did all the steps...

28 July 2024 2,136 4 View

How to prepare a molecule for molecular dynamics calculations?

If I want to calculate molecular dynamics (Gromacs), do I first need to optimize the geometry of the molecule? For example, I first draw the molecule in Avogadro, and then what? I guess I can't...

28 July 2024 673 3 View

Juan Carlos Muñoz García

Thank you very much Stephane. It seems to be what I'm looking for.

Massimo Sandal

A quick-and-dirty approach could be using MODELLER (the homology modeling software). MODELLER can work with just the C-alpha positions in the PDB and the sequence, and from there it can reconstruct an all-atom PDB. Just use your coarse grained PDB as a template.