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...

09 October 2016 8,294 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...

09 October 2016 7,732 15 View

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

08 September 2016 806 8 View

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

31 December 2015 1,367 12 View

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

31 December 2014 5,829 5 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?...

09 October 2014 9,178 4 View

How do I get RESP charges from antechamber?

09 October 2014 7,681 10 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...

06 July 2014 9,597 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...

04 May 2014 9,903 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...

04 May 2014 2,732 4 View

error in running a model in Abaqus

Excessive rotation of nodes in node set ErrNodeExcessRotation-Step1

17 August 2021 0 0 View

error in modelling model in Abaqus

Excessive rotation of nodes in node set ErrNodeExcessRotation-Step1

17 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MGL tools

20 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

flexibility of polymers chain

effect of double bond on the flexibility of polymers

07 April 2021 0 0 View