From: James Starlight (jmsstarlight_at_gmail.com)
Date: Sat Apr 12 2014 - 01:53:35 CDT
I also looking for the possibility to calculate free energy of ligand
binding using MMPBSA.py script and NAMD trajectory.
As I know in NAMD I can make parametrization of my system using amber (not
charmm) force field. So I need (i) proper way to parametrize ligand in
amber (ii) convert dcd to amber-like trajectory
Thanks for help
2014-04-10 19:09 GMT+04:00 Fotis Baltoumas <fbaltoumas_at_biol.uoa.gr>:
> Dear Srivastav,
> 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).
> Good luck,
> > Dear All,
> > In order to study the allostery of a protein system, we performed
> > molecular dynamics simulations using NAMD. We would now like to study the
> > conformational free energy landscape of the protein using MMPBSA.
> > the only one that we could find was the MMPBSA.py script in AMBERTOOLS
> > 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.
> > Regards,
> > Srivastav Ranganathan
> > Research Scholar
> > IIT Bombay
> > Mumbai, India
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