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

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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...

10 November 2017 8,029 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,...

11 December 2016 9,326 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 9,914 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 5,204 4 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 3,670 8 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 1,949 3 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 8,537 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 5,110 2 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 6,302 2 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 4,544 11 View

How can I prepare virus for a TEM or SEM imaging?

I have virus (viral hemorrhagic septicemia virus) in suspension and the experiment will not involve cells. What level of TCID50 is preferred?

11 August 2024 3,115 1 View

How to learn more about SPSS and its Application?

I would like to learn more about SPSS and Its application especially in regards to data analysis. Please suggest me how I can learn more about it. Thank you so much.

11 August 2024 9,101 4 View

Can I base on reverse DNA sequences to perform alignment, convert to amino acids and GenBank submission?

I have reverse sequences (AB1 format), can I base on reverse DNA sequences to perform nucleotide alignment, convert nucleotides to amino acids and deposit the sequence in GenBank database?

11 August 2024 5,138 1 View

Baseline drift in HPLC? What causes this?

Hello, Why do i see this baseline drift when i compare my blank (black) to the sample (blue)? Any suggestions as to why this happened? Thank you!

11 August 2024 3,770 4 View

Text-Communication from the M1 Hand Area using BCI—and then there is Elon Musk?

Willett, Shenoy et al. (2021) have developed a brain computer interface (BCI) that used neural signal collected from the hand area of the motor cortex (area M1) of a paralyzed patient. The...

10 August 2024 7,180 0 View

Handling Missing Data and Building a Predictive Model with Incomplete Information ?

I am developing a predictive model for a water supply network that involves 20 influencing points. However, I only have historical data for 10 out of these 20 points. I would like to know how to...

10 August 2024 4,005 2 View

Has anyone applied Python in the field of textile engineering for data analysis, automation, or smart textiles?

I'm currently exploring the application of Python in textile engineering, specifically in areas like data analysis, process automation, and the development of smart textiles. I'm interested in...

10 August 2024 7,429 2 View

Is it possible to use the Fused Deposition Modeling (FDM) to additively manufacture interconnected porous structure generation of >100-200 micrometer?

Usually, additive manufacturing techniques like SEBM, SLS, and SLM are used for interconnected porous lattice structure generation with sizes of >100–200 micrometers. Can the Fused Deposition...

09 August 2024 7,892 0 View

How can I use the cif data obtained from rietveld refinement extracted via gsas2, for microstructural analysis using ETEX software?

09 August 2024 7,718 0 View

How to define an anisotropic material with asymmetric elastic compliance/stiffness matrix in ANSYS APDL?

I need to model an anisotropic material in which the Poisson's ratio ν_12 ≠ ν_21 and so on. Therefore, the elastic compliance matrix wouldn't be a symmetric one. In ANSYS APDL, for TB,ANEL...

09 August 2024 5,048 2 View

Arafat Rahman Oany

You may try this

http://accelrys.com/products/discovery-studio/

Chanakya Nugoor

do you have MolMol or Pymol software available for free for academic researchers. I personally like Pymol as i love the way it can show visualizations. In Pymol, for one can allow only one chain you ask it to disply one chain and save the pdb file with one chain only as a new pdb. i assume it can do for the DNA also as i never worked with protein DNA complex, Nevertheless its worth a shot.

Leandro R. Jones

This paper could be a nice starting point:

http://www.sciencedirect.com/science/article/pii/S1046202313002053

Agnivo Gosai

Thanks everyone.