From: James Starlight (jmsstarlight_at_gmail.com)
Date: Mon Apr 14 2014 - 00:56:50 CDT
Many thanks for suggestions!
I'll try to wait AmberTools 14 and test it with the namd's produced
trajectory and all input files.
One question: can I use parametrization of my system done in charm-like
force field instead of amber (including ligand parametrized in cgenff)? As
I noticed amber need slightly shorter cutoffs for non-bonded terms in
comparison to charm indication difference in this terms between both force
Thanks for help,
2014-04-12 15:53 GMT+04:00 Jason Swails <jason.swails_at_gmail.com>:
> On Sat, Apr 12, 2014 at 2:53 AM, James Starlight <jmsstarlight_at_gmail.com>wrote:
>> 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
> For (i) you can use antechamber from AmberTools. Your step (ii) is
> unnecessary. MMPBSA.py understands DCD files natively.
> Also, if you've used the CHARMM force field and created the PSF file with
> VMD, the upcoming release of AmberTools 14 (within a week) will have a
> version of "chamber" that can convert VMD-generated PSF files into topology
> files MMPBSA.py can understand.
> Hope this helps,
> Jason M. Swails
> Rutgers University
> Postdoctoral Researcher
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