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

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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

Save VMD's contact map data in other formats besides postscript ?

VMD's contact map plugin allows me to save the data in postscript format, but is there anyway I can write out the data straight from VMD's Tk console or something so that I can plot the data...

11 December 2017 8,658 0 View

Can I use a HisTRAP column for affinity chromatography?

I'm working on selecting antibodies against a recombinant protein that has a His-tag. My idea is to first bind the recombinant protein to a HisTRAP column and then use this column for an affinity...

07 August 2024 505 3 View

Gromacs first step of minimization ?

I have face this problem anyone help me how to solve this issue ?which is below Fatal error: There are inconsistent shifts over periodic boundaries in a molecule type consisting of 78 atoms. The...

07 August 2024 2,598 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

What is the best blank for nanodrop if I want to read a recombinant protein concentration?

Is it the "elution buffer" or the "dialysis buffer"? Note: I'll be using NanoDrop OneC

01 August 2024 967 3 View

Can we patent a process flow diagram developed using a process simulator but no actual cases is carried out?

Can we patent a process flow diagram developed using a process simulator but no actual cases is carried out? For example consider a process for certain product manufacture where a new process flow...

31 July 2024 781 1 View