Radhika Geethu

20 Questions 60 Answers 0 Followers

Questions related from Radhika Geethu

How to choose the proper PH and temperature in the simulation of G-quadruplex DNA with anticancer drug?

Dear Researchers, There will be an impact in the binding of G-quadruplex DNA with the anticancer drugs due to different PH and temperature environment in our body. During the simulation how these...

10 October 2016 8,352 3 View

How to evaluate delocalization index ?

Hi Friends, I want to calculate delocalization index between the atoms involved in hydrogen bonding. I have an output of AIM analysis using MORPHY software. But I don't know to evaluate it. So I...

10 October 2016 7,805 15 View

What could be done to avoid the disruption in DNA during MD simulation?

Hi Friends, As I wanted to do structural studies of amonafide with the DNA sequence D(CCTGGTCC):D(GGACCAGG), I have done MD simulation in Gromacs with the force field amber99sb ildn. This DNA...

09 September 2016 874 8 View

Does docking of a telomere with a ligand is reliable using blind docking method?

Dear Friends, I used auto dock vina to dock telomere with a ligand. As I don't know which guanine in the G-quadruplex could be much specific for that ligand, I have done blind docking. But the...

01 January 2016 1,417 12 View

How do I get the DNA sequence from specific cell lines?

Recently I have referred a journal in which 1,8 Naphthalimide derived drugs were active on the HeLa cell lines. I am doing simulation work of DNA-anticancer drug interaction. I want to know how to...

01 January 2015 5,883 5 View

How do you solve the inconsistency #1 in MMType error in Gaussian 09?

I am running an ONIOM calculation using Gaussian 09, but the output / log file shows the "Inconsistency #1 in MMType error". I tried with all possible changes in the input file, but was unable to...

12 December 2014 2,039 7 View

How do I get RESP charges from antechamber?

I am dealing with DNA-drug interaction studies. For the simulation I am using amber 03 force field in GROMACS 4.5.5 . To parametrize the ligand Quercetin I am using antechamber. I am trying to...

10 October 2014 7,766 10 View

How to separate the charge groups in Gromacs?

Hello Friends, I have created an itp file for a drug by using PRODRUG. After that I have changed the charge values of the file (Using DFT). Now it is necessary to change the charge groups too?...

10 October 2014 9,279 4 View

Which is the most reliable software to find the active site in DNA ?

Dear friends recently I came to know about the software Q-site finder which find the active sites of protein for drug interaction. Is there any software for the same purpose in DNA too? Depending...

07 July 2014 9,652 3 View

Can anyone tell me how to plot spectra of absorbance vs wavelength?

I am doing drug-DNA interaction studies theoretically. I have done uv absorption job which is attached herewith. From the output I couldn't get the absorbance value directly. Someone told me by...

05 May 2014 9,956 8 View

Are results from the "Hex Protein Docking Server" reliable?

Recently I used the website "Hex Protein Docking Server". But I am suspicious whether the results are reliable or not . Also can it consider all types of binding (intercalating and groove...

05 May 2014 2,797 4 View

What is the relationship between absorbance and oscillator strength?

I am doing spectroscopic studies on drug - dna interaction (theoretically). I want to know the absorbance values in terms of wavelength in the UV-absorption studies for a comparison purpose. But I...

04 April 2014 6,417 11 View

Can anyone help me find pdb files of nucleotides?

I am doing drug - DNA interaction studies. For that I am in need of pdb files for di, tetra, hexa and oligo nucleotides (NMR structures are preferential). I didn't get some of the sequence of...

03 March 2014 3,471 6 View

How do can you find the chemical shift values of DNA base pairs?

I intercalated a drug with the base pairs AT,AA,GC etc (theoretical work). Then I have calculated the chemical shift values of the base pairs without drug and with drug. There is changes between...

02 February 2014 10,020 2 View

Can anyone advise on the distance dependent dielectric constant?

I am doing interaction studies of dna-drug. I want to know, what is the difference between distance dependent and distance independent dielectric constant? Also I want to know whether there is a...

01 January 2014 2,087 2 View

Is charge modification in the phosphorous needed in the optimization of DNA?

I want to optimize the DNA ds (CCTGGTCC) structure with an organic drug by using ONIOM (phosphorous in the low level amber force field). As we know that phosphorous is a negatively charged one:...

11 November 2013 300 8 View

Why some pdb files are not accepted by GaussView?

I am doing Drug-DNA interaction studies. For that I have selected a sequence of d(GGCCGGCCGG):d(CCGGCCGGCC). I have tried to get it from many data sources but no use. Finally, I got the structure...

11 November 2013 2,149 5 View

Can anyone please help me regarding to drug-DNA interaction?

I am working on Drug-DNA interaction. For this study I have selected a platinated drug with DNA and I applied 2 layer ONIOM technique. For the platinum atom I used SDD and effective core...

10 October 2013 4,447 1 View

Can anybody please tell me which software will be useful in the separation of DNA helix ?

Is there any free software available for this purpose?

08 August 2013 3,315 8 View

Can anybody help about optimization of molecules by using gaussian?

Actually i am so new to this field i am using chem craft for optimization.But i couldn't find proper way to optimize even for the small reactions. After processing completed ,i am getting wrong...

07 July 2013 5,321 13 View