Agnivo Gosai

14 Questions 43 Answers 0 Followers

Questions related from Agnivo Gosai

What could be the "physical significance" for the electrochemical circuit used to model EIS data ?

Hello, I have a two compartment electrochemical cell. I have put a nanoporous aluminum oxide membrane (nominal pore diameter = 20 nm) between these two compartments. Now I looked at the impedance...

11 November 2017 7,990 4 View

Is there a thermoresponsive liquid that does not mix with water?

Hello,I am looking for a thermo-responsive liquid which will not mix with water. The idea is to have two small connected reservoirs , one containing this liquid and the other having water. Then,...

12 December 2016 9,295 3 View

Is there a software tool for creating biomolecular structure for MD simulations ?

Is there any software tool to create the following : (1) DNA nulceotides with one S-H (thiol) group at its tail (2) To form an Au-S bond between the thiol and a layer of gold atomsI would like to...

01 January 1970 9,869 7 View

How to create a ss DNA structure having a quadruplex in PDB format ?

Hello , I want to create a PDB file for a ss DNA molecule having a quadruplex in it. I have checked the web and also here and got to know about a few webservers / softwares which can be used to...

01 January 1970 4,485 4 View

How to use make_ndx in GROMACS version 4.5.7?

I am using GROMACS version 4.5.7 and in my topol.top file there are 3 chains in the [molecules] section. Of these , two are protein chains. How can I use make_ndx to combine both the chains into a...

01 January 1970 8,505 2 View

How can I set up temperature gradient between protein and water by using thermostat in GROMACS?

Dear all, I am I am looking to replicate the figure attached with this post. The paper attached tells that the authors established a temperature gradient between a protein ( which cooled to 300 K...

01 January 1970 2,066 2 View

How do I add a new DNA residue to the terminus of my DNA PDB ?

I want to add a new DNA residue to the existing terminus of my DNA PDB file. How can I go about this task?? Can I use PyMol or Chimera ?

01 January 1970 5,062 2 View

How to calculate the mean force from PMF values?

I have a Potential of Mean Force (PMF) values obtained against a reaction coordinate in a file. This was generated using a pulling molecular dynamics simulation. I am thinking of taking numerical...

01 January 1970 3,613 8 View

How do I create a Au-S bond on a layer of gold in PDB format for use in MD simulations ?

I have created DNA and protein residues in Chimera for use in MD simulations. I would like to know about different ways to create a layer of gold atoms and a Au-S bond in PDB format so that it can...

01 January 1970 6,265 2 View

Can I use PRODRG for generating a GROMACS compatible topology file for a non standard nucleic acid?

My nucleic acid PDB file consists few non standard residues where the uracil, cytosine bases have been modified by adding methyl, phenol etc groups to them. Can I use PRODRG to generate a topology...

01 January 1970 1,914 3 View

Why is my topology not correct ?

Hello everyone, I am trying to run a MD simulation for a non-standard ssDNA molecule. As it had many nonstandard residues I used ACPYPE and Antechamber to prepare GROMACS compatible topology. I...

01 January 1970 5,444 8 View

I have a PDB file in which many protein residues are missing and this produces an error when I use pdb2gmx (GROMACS) , what can I do to fix it?

The protein is missing many residue parts and when I used pdb2gmx with the -maxwarn function I found that the total charge on the protein was + 5.269 electron units. How can I go about in fixing...

01 January 1970 4,510 11 View

What could be the possible cause for decrease in "charge transfer" resistance upon immobilizing SAM on gold coated glass?

Brief system description : Gold coated glass slide is the working electrode. Used an Al foil clamped to the Au coated glass for connecting to the working electrode of the potentiostat. A part of...

01 January 1970 8,986 7 View

How to measure the current flow across a membrane ?

Hello,I have an electrochemical cell consisiting of two chambers. These two chambers are separated by a membrane.Now, I want to observe the flow of current across this membrane for different...

01 January 1970 5,159 4 View