Prakash Jha

18 Questions 15 Answers 0 Followers

Questions related from Prakash Jha

Can any body know how to use latest version of Gromacs in CDAC-BRAF server..?

How I use the installed version of Gromacs 2018 from my home directory in CDAC-BRAF server? Please help me out..

09 September 2018 4,022 1 View

How can I get image file from .dssp file for secondary structure prediction?

I'm using DSSP 2.0.4. command I used: dssp.exe -i 6NUL.pdb -o 6NUL.dssp what it is the next command to get the image file? Please give me suggestion..

08 August 2018 10,127 0 View

How to perform hbond analysis between ligand and catalytic residues of receptor in gromacs ?

Hydrogen bond analysis

07 July 2018 6,469 2 View

MD simulation of protein-ligand complex using the Gromacs program available at The Bioinformatics Resources & Applications Facility (BRAF) at C-DAC?

I have taken The Bioinformatics Resources & Applications Facility (BRAF) at C-DAC. But donot know how to use it for MD simulation of protein-ligand complex using Gromacs program. Could...

05 May 2018 356 6 View

How can I simulate docked protein complex with pdb water. As these water molecule important in binding of the molecule ?

gromacs

05 May 2018 2,044 0 View

How to do simulation on BRAF server??

How can I transfer my files from my university server to BRAf server to perform MD simulation and how can I use environment module ??

04 April 2018 8,819 1 View

How to correct "step 12: Water molecule starting at atom 61920 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate" ?

Program gmx mdrun, VERSION 5.1.2 Source code file: /build/gromacs-z6bPBg/gromacs-5.1.2/src/gromacs/mdlib/constr.cpp, line: 555 Fatal error: step 12: Water molecule starting at atom 61920 can not...

04 April 2018 4,094 0 View

How to put constraint in the receptor ligand interaction during MD simulation in Gromacs?

I am follow this tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html In my case, protein with ligand simulated for 3ns. But after simulation the...

11 November 2017 6,355 6 View

Problem with make_ndx command in protein- ligand MD simulation.

There is zinc in a catalytic site. So, I merge Protein_Zn_Ligand by using command: gmx make_ndx -f em.gro -o index.ndx > 1

08 August 2017 7,133 2 View

How to get receptor- ligand binding energy graph in gromacs after successful md run?

what is the command for it???

08 August 2017 7,127 1 View

How to prepare for the csir net life science?

life science

09 September 2016 1,110 0 View

I have problem in topology organization during membrane protein simulation in gromacs. How to resolve this?

MD simulation

05 May 2016 7,580 0 View

How i extend the simulation time from 1ns to 2ns in gromacs?

molecular dynamics

04 April 2016 4,985 6 View

After this command "perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat" which file i used for em in membrane simulation ?

molecular dynamics

04 April 2016 5,475 2 View

How i do energy minimization of selected residue in gromacs?

Simulation

04 April 2016 9,383 0 View

How to check that how much time remaining for completing the simulation in gromacs?

md simulation

03 March 2016 4,882 3 View

Where did malaria come from first time in humans?

09 September 2015 2,635 1 View

How choose active water from all the water option in gold suite?

07 July 2015 3,906 0 View