Thank you Dwight
I tried your suggestion as follows:
mpirun -np 48 MMPBSA.py.MPI -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -slp lig_solv.prmtop -lp lig.prmtop -yl *.nc
mmpbsa throws the following error:
IOError: Could not open complex_prmtop for reading
Error occured on rank 1
Any suggestions?
George
> On 21 Oct 2015, at 18:53, Dwight McGee <dwight.mcgee.gmail.com> wrote:
>
> Hi,
>
> If you are using the triple trajectory approach, the flags for the ligand
> are *-yl* {ligand solvated traj} and *-slp* {ligand solvated prmtop}.
>
> Regards,
> Dwight
>
> On Wed, Oct 21, 2015 at 11:19 AM, George Tzotzos <gtzotzos.me.com> wrote:
>
>> I’m trying to compare the delta-G of binding of a complex using the
>> single- and three-trajectory approach.
>>
>> In the single trajectory approach, as per manual, th command used was:
>>
>> mpirun -np 48 MMPBSA.py.MPI -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat
>> -sp cmplx_solv.prmtop -cp cmplx.prmtop -rp rec.prmtop -lp lig.prmtop -y *.nc
>>
>> To get a more accurate estimate of the desolation parts of the energy of
>> the receptor and ligand, I’m trying to use the three trajectory approach. I
>> have run separate trajectories of the complex and one of the subunits.
>>
>> I looked at the manual but could not find an appropriate flag for the
>> solvated ligand file.
>>
>> I’d be grateful for any advice on the correct usage.
>>
>> Regards
>>
>> George
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>>
>
>
>
> --
> T. Dwight McGee Jr.
>
> dwight.mcgee.gmail.com
>
> "Problems cannot be solved at the same level of awareness that created
> them."
> Albert Einstein
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Received on Wed Oct 21 2015 - 09:30:03 PDT
