Thank you Dwight,
Now, it’s clear.
Best wishes
George
> On 21 Oct 2015, at 19:31, Dwight McGee <dwight.mcgee.gmail.com> wrote:
>
> Hi George,
>
> You will need to provide MMPBSA.py the following:
>
> mpirun -np 48 MMPBSA.py.MPI -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat
> -sp {solvated complex prmtop} -srp {solvated receptor prmtop} -slp
> {solvated ligand prmtop} -cp { dry complex prmtop} -rp
> { dry receptor prmtop} -lp { dry ligand prmtop} -y {complex traj} -yr
> {receptor traj} -yl {ligand traj}
>
> HTH,
> Dwight
>
>
>
> On Wed, Oct 21, 2015 at 12:10 PM, George Tzotzos <gtzotzos.me.com> wrote:
>
>> 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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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> _______________________________________________
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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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> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Wed Oct 21 2015 - 10:00:06 PDT
