How to convert .mol format into .mol2 format using OpenBabel ?

More Roshan Shrestha's questions See All

Gaps/Voids seen in POPC bilayer during MD simulation ?

Hi all, I am working on a MD simulation of a membrane protein inside the POPC bilayer using namd. At first, I ran a short constrained dynamics by applying harmonic constraints to both...

05 June 2019 7,435 4 View

Check if the lysine residues are deprotonated or not inside the membrane ?

Hi everyone, My system is a dimer. During the MD simulation, I can see a strong hydrogen bond formed between two lysine residues which are at the side chains of two peptides. But, the issue is...

04 May 2019 6,105 5 View

PDB manipulation options in Charmm GUI?

Hi everyone, While using the PDB reader of charmm-gui for my membrane protein system which is a dimer, I got stuck at PDB manipulation option. It gives me option regarding...

04 May 2019 2,487 3 View

Protein-lipid interaction ?

Can anyone please suggest me review articles/papers/books/links on understanding protein-lipid interactions through Molecular Dynamics simulation ? Thanks

01 February 2018 4,939 3 View

Definitive non-bonded distance to form a contact ?

Is there any standard value like two non-bonded residues or atoms are considered to form a contact if their distance is less than ? I usually use like 1.4 nm for short range non-bonded LJ cut-off...

01 February 2018 9,846 4 View

Plotting running average in python similar to in Xmgrace ?

Are there any scripts or tools available in python to plot the running average of the data similar to as shown in the figure attached? Thanks

31 December 2017 2,525 4 View

Rotate a specific residue and save the coordinates in VMD ?

I want to rotate a specific residue (say "resid 7 and resname MET") by 180 degrees around x-axis and save the coordinates. Can it be done using VMD's TK Console ?

31 December 2017 7,579 7 View

Thermal vibration of bonds ?

The characteristic frequency of thermal motion is around 7E12 Hz at room temperature (300K), but from that information how can we conclude that the bonds are hard; they don't vibrate !!

31 December 2017 6,084 2 View

Measurement of helical tilt (dimer tilt) using gmx helixorient ?

I want to measure the tilt of helix with the normal of bilayer. My system is basically a dimer with two helices. Since using sidechain atom relative to the axis is optional, I simply defined...

31 December 2017 730 3 View

Gromacs tool or any tools to look for the number of protein-lipid contacts ?

Are there any gromacs or other tools available to look for or find the number of protein-lipid contacts during Molecular Dynamics simulation of membrane protein ?

11 December 2017 2,812 3 View

Can you suggest reliable sources defining "3D mesh" and "3D city models"?

Dear fellow researchers, I am currently working on a paper where I need to provide a reliable reference that defines and distinguishes between 3D mesh models and 3D city models. Although I am...

06 August 2024 9,986 2 View

What are the shear and normal stiffness values of an LLDPE liner in 3D numerical modeling of a stockpile?

I am seeking experimental or applicable data for the liner (LLDPE) interface in FLAC3D numerical modeling of a large stockpile. Could you please recommend suitable references? The preferred data...

05 August 2024 3,665 0 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

Why running a restart analysis in Abaqus in Ubuntu OS gives an error as attached when running the same job in Windows doesn't give any error and runs?

I am trying to run a restart analysis, which imports deformed configurations of parts from a generated ODB file. It runs fine in Windows OS but when I try to run it in Linux OS, it is giving some...

29 July 2024 9,572 3 View

Cell optimization in 1D Nanotubes?

Dear All, I use Quantum Espresso. I want to optimize the structure of the carbon nanotube using the vc-relax. I got confused about how to fix cell_dofree here. For 3D, cell_dofree = 'all' or...

22 July 2024 5,708 0 View

How to classify 3D Bioprinting as a part of Additive Manufacturing?

Hello, I have a problem in classification of "Additive Manufacturing" techniques. There are several classification for Additive Manufacturing e.g. Powder, Extrusion, Resin etc. Actually, I am OK...

15 July 2024 139 3 View

Which software use to i make this graph quickly and also make more dimensions of this graph( i mean adding vertices or lines in this graph)?

Anyone kindly tell the name of software that make this graph quickly and also tell how we add vertices or lines in this graph with equal distance to get next dimensions of this graph ( i mean how...

11 July 2024 4,499 2 View

Quelles applications innovantes peuvent bénéficier des propriétés des géopolymère?

Les géopolymères offrent plusieurs propriétés intéressantes qui peuvent être exploitées dans diverses applications innovantes : 1. Construction durable : - Bétons à faible empreinte carbone -...

10 July 2024 7,457 1 View

What should I upgrade in my computer to speed up simulation in CST?

I want to reduce simulation time in CST for frequency domain solver by upgrading my computer. I already have discrete GPU but it doesn't seem to make any difference at all compared to integreted...

10 July 2024 2,789 4 View

Can I transfer the 3D file from Matlab to Ansys or Abaqus?

I have a 3D output in the figure section of Matlab, does anyone know a way to transfer it to Abaqus or Ansys? Or in what format should I save it so that these analysis software can analyze it?

09 July 2024 9,226 3 View

Pranavathiyani G

You can use Online tool E-BABEL for file format conversion or you can follow the steps given in the link.

You can use ACD/ChemSketch or MarvinSketch also.

http://www.vcclab.org/lab/babel/

https://openbabel.org/docs/dev/Installation/install.html

http://www.webqc.org/molecularformatsconverter.php

Mokhtar Nosrati

Hi,

You can use Avogadro software.