Calculating Protein-lingand interation using MM/GBSA and MM/PBSA
You can have a look at the following link:
http://rashmikumari.github.io/g_mmpbsa/
Software uses trajectory created from gromacs.
This reference may also help:
http://pubs.acs.org/doi/abs/10.1021/ci500020m
Dear Hiqmet,
Thank you..
The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4487606/
http://www.sciencedirect.com/science/article/pii/S0010465514003154
Dear Anu,
Thank you.
I would recommend you to first try with files (.mdp) in tutorial. This will minimize errors
Dear Kumar, can you attach the .mdp file or link the tutorial so that I can access...
Dear Shadrack
Find it here http://rashmikumari.github.io/g_mmpbsa/Tutorial.html
All the best
Thank you...
I am simulating Protein-ligand interaction using gromacs and now I am getting this problem. Please held how to fix it. Fatal error:Too many LINCS warnings (1001)If you know what you are doing you...
07 August 2017 4,122 8 View
Which force fields can I use to run molecular dynamics of PAMAM dendrimers in Gromacs??, I have tried different force fields in Gromacs with no success..
05 June 2017 7,668 1 View
How to calculate the RMSD values for a MD simulation using MOE?
07 August 2021 0 0 View
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
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
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
Dear all, I just saw this example in FB on the difference between laminar flow and turbulent flow. The flow from a pipe hits the sink and scattered. The flow from the pipe is characterized as...
02 March 2021 1,999 5 View
Hi In Molecular Dynamics Simulation, how do I make changes to the force field according to my protein? I got this error in the add-ion stage: Fatal error "./ amber99sb-ildn-HHH.ff / force...
01 March 2021 8,747 4 View