You can use either ParmEd or cpptraj to strip away atoms from a topology
file and generate a new one that will work with sander. So you can use
this functionality to get at the quantities you want (note the added
complexity if you are using periodic boundary conditions and PME for
electrostatics -- you need to be careful about exactly what you're
computing).
HTH,
Jason
On Thu, Jun 18, 2015 at 1:28 AM, loic etheve <loic.etheve.ibcp.fr> wrote:
> Hi,
>
> I have a restart/pdb from a protein/dna complex file from minimisation
> and i want to know if it exist a way or a tool that allow me to
> calculate internal energy for dna alone, protein alone and complex using
> this restart/pdb file without make mm_pbsa calculation ?
>
> Loic
>
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>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Jun 18 2015 - 07:00:02 PDT
