On Mon, May 11, 2015 at 2:52 PM, George Tzotzos <gtzotzos.me.com> wrote:
> I’m trying to find deltaG of a homodimer.
>
> The dimer contains chains A (res 1-125) and B (res 127-151), two conserved
> water molecules (res 153,154) and two ligands (res 126, res 152).
>
> I used ante-mmpbsa.py to generate new topologies:
>
> ante-mmpbsa.py -p complex_solv.prmtop -s :126,252-254,WAT,Na+ -c
> subA-subB.prmtop -m :1-125 -r subA.prmtop -l subB.prmtop --radii=mbondi2
>
I'll just point out that this gets rid of the conserved waters, in case
you didn't know that (since you stripped all WAT residues).
> I tried to run mmpbsa.py (serial) for a short 10 frame trajectory as test.
>
> MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp
> complex_solv.prmtop -cp subA-subB.prmtop -rp subA.prmtop -lp subB.prmtop -y
> 10frame.nc
What is "strip_mask" set to in your mmpbsa.in file? It *should* be the
same as what you fed to ante-MMPBSA.py via the "-s" flag. If it's not,
then only waters and ions will get stripped, and the resulting complex
trajectory will not match the complex prmtop you generated above.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon May 11 2015 - 12:30:03 PDT
