You can do this by simply not providing a ligand or receptor prmtop file to MMPBSA.py. But you do still need to supply a dry complex file for the system.
I hope that helps.
-Bill
On Jun 18, 2014, at 5:53 PM, <Andrew.Warden.csiro.au> wrote:
> Hi,
>
> I am running into problems with the apparent requirement for a ligand.prmtop, complex.prmtop, solvated.prmtop in MMPBSA.py when I just want to calculate the energy contribution per residue over an MD trajectory. Is there some way around this? For reference, I want to simply run:
>
> Input file
> &general
> startframe=1000, endframe=2000, interval=50,
> verbose=2, keep_files=0,
> /
> &gb
> igb=5, saltcon=0.1,
> /
> &decomp
> idecomp=1, print_res='1-1456',
> /
>
>
> Many thanks for your help.
>
> Andrew
>
>
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Received on Wed Jun 18 2014 - 16:00:02 PDT
