Abhishek Tyagi

10 Questions 70 Answers 0 Followers

Questions related from Abhishek Tyagi

Gaussian cub output is not overlapping with isosurface ?

I want to do Bader charge analysis and I have observed that the cub file generated from gaussian have problem in overlapping to its surface when opened in Vesta. any suggestion what could be done...

21 August 2018 4,693 3 View

Interaction energy from md trajectories.

I used namdenergy plugin in vmd to extract total, vdw and electrostatic energy. I am confused to know about the energy provided by apbs/mmpbsa. How it is different from the data obtained from...

14 October 2016 3,605 2 View

How to make double stranded cDNA from single stranded cDNA?

I want to make cDNA library from RNA. I am using QIAGEN kit to get a cDNA, however the product obtained is single stranded cDNA. Can anyone suggest me how to convert this single strand cDNA into...

12 April 2016 608 8 View

What kind of raman shift could be observed from peptide?

I had a peptide, I am trying to get raman spectra of peptide, I found in literature, the shift in peak could be observed. What kind of shift could be observed red/blue and Why? I had done some...

06 October 2015 4,789 5 View

Can we do umbrella sampling and SMD by CHARMM or NAMD?

I want to do Umbrella Sampling (US) using NAMD, my confusion is as follows: 1. US can be perform using SMD, therefore, how to decide the SMD config file input is correct or not? What input CV or...

09 November 2014 7,056 3 View

Can anyone help me to design a new force field for a small organic/inorganic molecule for NAMD?

I want to attach a molecules with the biomolecule, but unfortunately I do not have the reasonable force field for this molecule. Now what I tried for to get force field is as follows: 1. I tried...

15 July 2014 9,335 16 View

If we want to know the result output from a NAMD simulation, what different results could be obtained?

I am new to NAMD and recently run a simulation of DNA-organic molecule interactions in NAMD for 20 ns. I want to know what the different results are that I should analyze using the output of the...

23 June 2014 9,552 5 View

How protein interaction with other ligands are estimated and analysed?

In in silico studies what could be good softwares and servers to analyse these interactions?

12 February 2013 7,152 2 View

What are different Protein-Protein interaction software/servers?

the softwares and server avalable?

18 December 2012 1,635 12 View

Tools for Molecular dynamics simulation?

Please tell me tools for molecular dynamics simulation studies. Software for Windows and Linux platform, free and commercially available.

17 December 2012 5,853 49 View