g_mmpbsa Mailing List

Hello users, I have a protein complex with more than 2200 residues , a ligand binding to the protein

These commands I have used sequentially...but command no. 4 is not completed yet after 4 days...how

When you sometimes conduct an MD simulation with poorly optimized ligands, the calculated energies

I hope you are well. Very sorry for my email. My name is Asmar Kabani. I have done GMMPBSA and in my

I started my g_mmpbsa calculation on one PC, but it turned out to be very slow (3 ns/day). So I'd

Hi. I have gromacs 2019.6. I'm installing g_mmpbsa using the installation guide in the following

Hi, Did the ligand leave completely the pocket or it found another pocket..? There are some cases

Dear all, I am trying to do a polar molecular calculation with the Gromacs-5.1.x include APBS

Hi, Thank you very much for your insight. For a protein-protein binding, which dielectric value

The protein has charge of -17 and ligand charge of +1. On Monday, January 18, 2021 at 3:31:26 PM UTC+

Very simple, Copy residuetypes.dat file from top directory of gromacs to your working directory. On

You can use VMD to convert from one format to another. On Thu, Dec 17, 2020, 17:50 S Muthu Raj <

Hi all I ran some jobs with gromacs 2020 mpirun and try running mmpbsa but the jobs were core dumped.

I am now trying to calculate the average and get the summary of free binding energy but this message

Dear Users, I have done a 300ns simulation of a protein_A-protein_B in complex with a bound small

Hi solved your problem? On Wednesday, June 13, 2018 at 2:01:49 PM UTC+4:30 Amal_porto wrote: Dear

Hello If you run g_mmpbsa for 100ns it will take forever even in supercomputers. The best way for

These commands which i have used sequentially...but command no. 4 not completed yet after 10 days...

Yes, solute dielectric constant in pbsa.mdp file should be same as in command line pdie option. pdie

Hi, do you keep to pdie value the same in the command line and in the .mdp file?

Dear .... Its an ideal results, its may be result from conformation of protein such as positive amini

Hi everyone, I want to calculate the binding energy of coarse-grained MD results, and is g_mmpbsa

It is common to have a positive polar solvation energy. It is compensated by negative electrostatic

It seems that the WCA method was partially the source of the errors being generated here. After

Also, please read this: http://redmine.gromacs.org/issues/2752. You might be trying to read tpr file

When I used g_mmpbsa to caculate polar sovaltion energy ,I got many errors. This is my code :g_mmpbsa

Hi everyone, I am a freshman to use g_mmpbsa tool for Protein-ligand binding energy analysis. One

Hi everyone! I just want to use g_mmpbsa tool for protein to protein binding energy calculation. And

Hi! I am not sure I have a solution to this because I haven't worked on metal nanoparticles. Btw,

#Complex Number: 1 =============== SUMMARY =============== van der Waal energy = -210.718 +/- 22.169