09 September 2015 1 3K Report

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More Prakash Jha's questions See All
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..

08 September 2018 3,934 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..

07 August 2018 10,024 0 View

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

Hydrogen bond analysis

06 July 2018 6,357 2 View

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

gromacs

04 May 2018 1,983 0 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...

04 May 2018 212 6 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 ??

03 April 2018 8,735 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...

03 April 2018 3,933 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...

10 November 2017 6,296 6 View

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

what is the command for it???

07 August 2017 7,057 1 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

07 August 2017 6,919 2 View

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