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 7,291 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 5,965 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 2,169 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 4,797 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 9,699 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 2,318 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 7,382 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 5,947 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 457 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 2,664 3 View

What software programs can directly simulate Additive Manufacturing Directed Energy Deposition (DED)?

I understand there are a lot of software programs that can simulate DED by going through specific modeling, simulation, and commands. For me, that was time consuming and results were not accurate....

24 February 2021 4,428 3 View

I am looking for a simple software program to model 3D chemical bonds. The purpose is to generate high-quality graphical abstracts. Any suggestion?

Hello everyone: I am looking for a simple software program to model chemical bonds. The purpose is to generate a high-quality graphical abstract for a top leading journal in the field of...

23 February 2021 8,012 3 View

How can I retrieve FASTA sequence from gene ID or UID of a Gene ? I have GeneBank IDs ?

I treid to use Entrez Batch, but it redirects me to NCBI site. Is there any script of Linux or Python through which I can download Fasta sequence of list of gene ID ?

21 February 2021 7,783 12 View

Which programs are to be used to register 2D image onto a 3D image data set?

I am trying to register a light micrograph onto a 3D CT data set, as I want to extract the corresponding image from the CT data set. Is there any software or program can do this accurately? I am...

21 February 2021 8,220 3 View

What is the better software for approximation of 3D surface with equations?

I have a massive of x, y, z coordinates of 2D surface in 3D space, which builded in Ansys HFSS or AutoCAD. How can I get the analitical aproximation of this surface by formulas?

21 February 2021 3,444 7 View

How can I obtain Reaction Forces in ABAQUS?

I am trying to simulate a simplified version of a beam resting on 10 points using Abaqus. The solutions I want to obtain are the Reaction Forces in each resting point or area when applying a...

21 February 2021 3,075 2 View

How to convert 2D stack images to 3D to obtain surface area of nucleus?

I have 15 slices of the nucleus at different z-heights from confocal imaging. I would like to use these slices to reconstruct the 3D nucleus and ultimately estimate the surface area of the...

20 February 2021 6,967 1 View

How to get the vector of a specific vibration mode in phonon dispersion?

For example, I have this phonon dispersion(Fig. 1), and now I would like get vector of atoms which describes TA1 in P. I know v_sim can show vibrational animation of specific mode, but I do not...

20 February 2021 4,332 4 View

Has anyone used deep learning for 2D/3D REGISTRATION ?

I am a Master student in Biomedical (Bio-electrical) Engineering and work on " 2D-3D registration ( CT and X-Ray) as my thesis. I created DRR from CT and want use CNN( Convolutional Neural...

19 February 2021 6,354 3 View

PV system design. 3d modelling and Analysis?

I have been looking for a good cost-effective tool for 3D modelling a glass-glass solar module system. I was initially considering Skelion as a tool but it does not look very promising, a bit...

13 February 2021 8,126 1 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.