One option may be considered if entropy is neglected:

=> psf2top can be use to convert psf file to gromacs format topology file. (https://github.com/resal81/PyTopol/wiki/psf2top-Usage)

=> catDCD can be use to convert dcd to gromacs format trr trrajectory file. (http://www.ks.uiuc.edu/Development/MDTools/catdcd/)

=>A GROMACS tpr file can be generated through grompp (A gromacs module)

=> Then g_mmpbsa can be use to calculate the binding energy through tpr and trr files. This tool does not include entropy calculation. (http://rashmikumari.github.io/g_mmpbsa/index.html)

I do not think you can do all necessary calculations using namd, you may need apbs for calculation of solvation energy, you may use vmd for mm calculations, and other software to do normal mode or quasi harmanic analysis for entropic calculations. In addition, you need other tools for sasa calculations.

But, if you convert your trajectory in a format acceptable for amber, you may use mm-pbsa tools of amber.

You need to download APBS software for calculating PB. APBS can be linked to NAMD during installation. A tutorial about how you can do it is found on installation documents for APBS and a tutorial about how to use APBS calculation with NAMD can be found on the NAMD tutorials.

One option may be considered if entropy is neglected:

=> psf2top can be use to convert psf file to gromacs format topology file. (https://github.com/resal81/PyTopol/wiki/psf2top-Usage)

=> catDCD can be use to convert dcd to gromacs format trr trrajectory file. (http://www.ks.uiuc.edu/Development/MDTools/catdcd/)

=>A GROMACS tpr file can be generated through grompp (A gromacs module)

=> Then g_mmpbsa can be use to calculate the binding energy through tpr and trr files. This tool does not include entropy calculation. (http://rashmikumari.github.io/g_mmpbsa/index.html)

Dear all,

I performed the g_mmpbsa analysis after great difficulty in installing the utility with the command:

g_mmpbsa -s md3.tpr -f md3.xtc

and the output was an energy file that I have attached herewith.

Is this the only output that the analysis gives?

I am apprehensive about this.

Kindly clarify.

@Revathi

The MM-PBSA method consists of three energy components: Molecular mechanics(MM), polar-solvation and non-polar solvation energy. You have calculated only MM energy.

To calculate other two components, you have to use option "-pbsa". You will need an input file for this calculation. For example:

g_mmpbsa -f md3.xtc -s md3.tpr -i mmpbsa.mdp -nomme -pbsa -pol -apol

"-nomme" suppresses the calculation of MM energy as you have already calculated it.

Details are provided in http://rashmikumari.github.io/g_mmpbsa/Usage.html#g_mmpbsa .

Keywords/parameters acceptable in mmpbsa.mdp file are described in http://rashmikumari.github.io/g_mmpbsa/Parameters.html

Once energy_MM.xvg, polar.xvg and apolar.xvg are obtained, "MmPbSaStat.py" script is required to calculate final binding energy.

I am running the g_mmpbsa analysis for my protein-ligand systems and I have 2 queries:

1. For a system size of 3 000 000 atoms, g_mmpbsa calculations take 1 week for 3000 frames ( I am running on 12 cpus and no gpus). In your opinion is this time equivalent to your bench marks?

2. I took the last 30 ns (15000 frames and skipped every 5 frames hence 3000 frames). Do you think 3000 frames is on the upper limit? What is the minimum and acceptable no. of frames for a meaningful mmpbsa output?

Kindly provide your valuable suggestions in this regard.

Thank you in advance.