Thank you Jason.
I had omitted the strip_mask in the mmpbsa.in file.
Regards
George
On 11 May 2015, at 21:00, Jason Swails <jason.swails.gmail.com> wrote:
> 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 - 12:30:04 PDT
