19 Questions 126 Answers 0 Followers
Questions related from Abhishek Tyagi
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...
08 August 2018 2,296 4 View
I want to simulate hairpin DNA with drug complex, but I found it difficult to design pdb file for hairpin DNA. I tried few available online resources but can not design, the sequence I am using is...
08 August 2017 2,427 7 View
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...
10 October 2016 3,512 3 View
I want to build graphene coarse grain system. I tried CG builder, but for CG builder I need initial pdb, that I tried to build using VMD nanotube builder, I can build the model, however when i...
05 May 2016 2,097 5 View
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...
04 April 2016 5,568 8 View
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...
10 October 2015 4,538 5 View
I want to calculate number of close contact and contact area calculation for a receptor-ligand interaction. I had performed MD using NAMD. I tried to search any VMD script for this, but not...
03 March 2015 3,172 7 View
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...
11 November 2014 5,550 3 View
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...
07 July 2014 9,078 16 View
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...
06 June 2014 2,075 6 View
I need to know the procedure and required tools for the construction .par, .inp, .tcl files
11 November 2013 7,048 2 View
Bilateral Lipid layer for membrane protein simulation at 70ns using Gromacs.
02 February 2013 4,767 6 View
In in silico studies what could be good softwares and servers to analyse these interactions?
02 February 2013 5,933 4 View
Gromacs, namd.. Etc
01 January 2013 8,061 12 View
In present scenario a lot of bioinformatics work is involved in biotechnology labs.
01 January 2013 863 6 View
Please tell me tools for molecular dynamics simulation studies. Software for Windows and Linux platform, free and commercially available.
12 December 2012 5,617 44 View
The protein is of 543 amino acids, its MD simulation is done using Gromacs, the problem is occurring when the duration is set for 1000 PS and contemporary steps. The problem occurs in 457 step...
12 December 2012 2,133 9 View
I am not sure about the approach, but I am interested to work in the area of System Biology. Please suggest me how to start work in this area. What are the minimum requirements to execute the...
12 December 2012 8,074 5 View
the softwares and server avalable?
12 December 2012 2,672 12 View
