VMD-L Mailing List
From: Fotis Baltoumas (fbaltoumas_at_biol.uoa.gr)
Date: Thu Apr 10 2014 - 10:09:00 CDT
I don't know whether there are any scripts. However, you can run MM-PBSA
calculations in NAMD using the iAPBS/NAMD module. As far as I know, iAPBS
is already implemented in the latest standard APBS distribution. iAPBS can
be coupled to NAMD through the appropriate module, and their user's guide
mentions the ability to perform MMPBSA. You can browse through the iAPBS
manual (http://mccammon.ucsd.edu/iapbs/usersguide/index.html), or you can
try the APBS mailing list/users group
(https://groups.google.com/forum/#!forum/apbs-users) for more information
(I have no experience with this type of calculations, so I cannot offer
any more help on that).
> Dear All,
> In order to study the allostery of a protein system, we performed targeted
> molecular dynamics simulations using NAMD. We would now like to study the
> conformational free energy landscape of the protein using MMPBSA. However,
> the only one that we could find was the MMPBSA.py script in AMBERTOOLS 13.
> Unfortunately, after a lot of attempts, we have still not been able to
> successfully run the calculations owing to some repeated format errors
> (CHARMM/XPLOR psf to AMBER prmtop). I would like to know if there are any
> MMPBSA post-processing scripts (in VMD or otherwise) that have been
> implemented to work with NAMD trajectories?
> Any help from the community on this would be greatly appreciated. Looking
> forward to your inputs.
> Srivastav Ranganathan
> Research Scholar
> IIT Bombay
> Mumbai, India