Re: Solvation free energy calculation with MM/GBSA

From: Abhishek TYAGI (
Date: Thu Sep 24 2015 - 07:13:20 CDT

Dear Neelanjana,

if you want to use AMBER GBSA method, its easy you need to follow their tutorial and modify your files accordingly, you need to convert the par and top file including sf pdb file to their format, this may not that accurate as we follow charm ff in NAMD, and when it converts to AMBER format it may some issues and dcd files will be used directly as input for trajectories. Although, they claim its OK.

You need to use chamber available in amber tool, freely available followed by mm-gbsa calculations for quasi harmonic approximation.

Further, you may check their mailing list and this issue was discussed several times over their.

Best wishes

Abhishek Tyagi

PhD Student

Chemical and Biomolecular Engineering

Hong Kong University of Science and Technology

Clear Water Bay, Hong Kong

From: <> on behalf of Neelanjana Sengupta <>
Sent: Wednesday, September 23, 2015 7:51 PM
Subject: namd-l: Solvation free energy calculation with MM/GBSA

Dear NAMD community,

We would like to calculate the solvation free energy, using the Generalised Born Surface Area (MM-GBSA) method, of a protein-nanosurface system that has been simulated with NAMD; we have the PSF file and the DCD files.

Could you suggest how to go about this? (The APBS method will only allow the PBSA method).

We are investigating options where we convert our trajectories to the AMBER format and use the utilities available there, but this is very messy...

Thanks in advance.


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