g_mmpbsa-1.6 version release

[g_mmpbsa Mailing List]

Release Notes 1.6 version :

   1. Added support for Gromacs-5.0.x versions

   2. Automatic detection of Gromacs versions. No need to write Gromacs version during compilation.

   3. Fixed -rvdw option

   4. Fixed warning "Setting option -pdie more than once!Ill"

   5. Python scripts work with both Python 2.7.x and and Python 3.x

   6. Tried to fixed Segmentation errors in Binary Packages (Happens due to different CPU architecture)

[rajan kumar choudhary]

how to get it

On Wednesday, 21 October 2015 15:36:31 UTC+5:30, g_mmpbsa Mailing List wrote:

Release Notes 1.6 version :

   1. Added support for Gromacs-5.0.x versions

   2. Automatic detection of Gromacs versions. No need to write Gromacs version during compilation.

   3. Fixed -rvdw option

   4. Fixed warning "Setting option -pdie more than once!Ill"

   5. Python scripts works with both Python 2.7.x and and Python 3.x

[g_mmpbsa Mailing List]

Download and Install it as written on the g_mmpbsa website (http://rashmikumari.github.io/g_mmpbsa/Download-and-Installation.html).

[Paulo]

How can the mutate_traj_tpr.py code be used? Could you provide some instruction? I cant figure out just based on the python code.

[g_mmpbsa Mailing List]

mutate_traj_tpr.py is an experimental script. We were trying to develop the method/protocol to calculate free energy for mutations (for Alanine scanning or any other mutations), but due to time constraints, we stopped working on it. Therefore, this script is not a complete functional script.

[Khushboo Singh]

Hi,

I using g_mmpbsa for calculating binding free energy for protein-ligand complex. 

No matter what value I choose for the option -rvdw the output (energy_MM.xvg) does not change at all. The command used is pasted below.  Is it because -rvdw option is not functional or am I doing something wrong. Please advise.

g_mmpbsa -f test.xtc -s test.tpr -n index.ndx -pdie 2 -decomp -mm test.xvg -mmcon test.dat -rvdw 0.9 

Thanks,

Khushboo Singh

Ph.D. Candidate

[Sinha Suman]

Hi,

Currently I am working on peptide protein systems. Is it possible to calculate binding energies of peptide ligands with this tool ?

[g_mmpbsa Mailing List]

Hi, 

Yes, It can be used for protein-peptide system. However, without considering the entropy, binding energy may or may not be comparable between different peptides. You can try and see how binding energy differs between peptides. Moreover, you can get residues that are favorable for binding.

With best regards,

g_mmpbsa team