How i do energy minimization of selected residue in gromacs?

Prakash Jha @Prakash_Jha14

04 April 2016 0 9K Report

Simulation

Badges
Science topic

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

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

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

How to analyze a particular region of my simulation box in GROMACS?

Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...

03 March 2021 9,989 2 View

After a reference from Int J Body Compos Res, can any body help?

Hi, I am after the reference below, my library says it cannot obtain a copy either locally or internationally, any help appreciated! Chris Wang ZM, Heshka S, Wielopolski L, Pi-Sunyer FX, Pierson...

03 March 2021 6,193 1 View

Irradiation data for JAPAN?

Hi, Could you help me to get the latest (2019, 2020) solar resource data for a particular site in JAPAN? PV GIS and NSRDB data are not in reach to JAPAN, I'm looking for some other database for...

03 March 2021 961 3 View

How to increase a model accuracy ?

dear community, my model is based feature extraction from non stationary signals using discrete Wavelet Transform and then using statistical features then machine learning classifiers in order to...

03 March 2021 6,994 5 View

Arena simulation - how do i model the following model in ARENA (see description) (new to ARENA)?

Hello, I'm fairly new to ARENA and I have the following problem: I have two queues in which, in each queue, a different order type arrives (both having an arrival rate of exponential 10). Order...

02 March 2021 2,431 3 View

Why are the velocities so high in my Boussinesq approximation Fluent simulation?

Hello, I have a mechanism where air rises due to convective flows. In this simulation, nothing is driving the air except this. I understand that the Boussinesq approximation only works for small...

02 March 2021 4,910 3 View