what is the command for it???
http://www.bevanlab.biochem.vt.edu/Pahttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.htmlges/Personal/justin/gmx-tutorials/complex/index.html
use gmx lie command for 5+ gromacs version or g_lie for 4+ gromacs
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
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
Hydrogen bond analysis
06 July 2018 6,357 2 View
gromacs
04 May 2018 1,983 0 View
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 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
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
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
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
life science
08 September 2016 977 0 View
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
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
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
hello everyone, I need to do standard curves for my qPCR, what is the ideal efficiency range? I tried a primer (Mglu2 receptor) that gave an efficiency of 90.2%. Is it accepted?
28 February 2021 1,254 3 View
When you use RIA, with a control the unknown sample with antibodies, you bare in mind the binding sites of the antibodies. However you still need to measure labelled antigen (radioactive) and not...
28 February 2021 2,133 3 View
Hi, I want to calculate the radial distribution function for water molecules around the Na+ ions adsorbed on the surface of a spherical nanoparticle using the gromacs trajectory dynamically? For...
28 February 2021 5,650 1 View
I have run a MD simulation of a ligand-protein complex in GROMACS using CHARMM forcefield. Reviewer has asked me to calculate Ligand-activesite distance and binding free energy of ligand with...
27 February 2021 4,703 1 View
Dear all, I am trying to perform a MD simulation about the interaction between CO2 and a polymer. I create my model, solvate it and perform the NVT and NPT equilibration. Now I am not able to...
26 February 2021 10,014 3 View
I want to get a average structure from a pdb file containing multiple models. I used the command below: gmx cluster -f input.pdb -s topol.tpr -cutoff 20 -method gromos -av GROMACS...
25 February 2021 6,314 1 View
Dear All, We are using Autodesk cfd to calculate the air flow in a single sided naturally ventilated room, where air flow depends only on buoyancy due to temperature difference between inside and...
25 February 2021 9,602 4 View