From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Sat Apr 12 2014 - 03:46:19 CDT
Take a look at AmberTools 13.0 manual. The "chamber" tool can be used to convert psf files to amber topology. The "cpptraj" tool can read dcd files and output netcdf trajectories that can be read by MMPBSA.py ...
A word of caution .... To use MMPBSA it is crucial to understand the radii used for the calculation (mbondi2 or others, see amber tools manual). The radii depend on the amber atom types assigned and the methods used within MMPBSA ... So you should check that carefully as well. You can use the tool "parmed.py" to edit your amber topology. Besides, you should make an effort to understand every single parameter used by MMMPBSA.py. I don't recommend relying on defaults. MMPBSA is not a trivial calculation and you can easily get wrong results.
When you are not experienced with AMBER please make an effort to understand it before embarking to sophisticated calculations. Using one tool requires some knowledge about the whole package.
Sorry for these details related to Amber but I saw this question coming up many times. A good idea is to search/subscribe to the amber mailing list as well.
Best,
Vlad
Sent from my android device.
-----Original Message-----
From: James Starlight <jmsstarlight_at_gmail.com>
To: Namd Mailing List <namd-l_at_ks.uiuc.edu>
Sent: Sat, 12 Apr 2014 9:18 AM
Subject: Re: namd-l: MMPBSA Energy Calculations using VMD (Post-Processing)
Dear all,
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
James
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,
> Fotis
>
> > 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.
> >
> > Regards,
> >
> > Srivastav Ranganathan
> > Research Scholar
> > IIT Bombay
> > Mumbai, India
> >
>
>
>
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