You are the best!!!!!!!!!!!!!!
It is working!!!!
Thank you!!!!!!!!!
Enviado desde mi iPhone
> El 24 ago. 2020, a la(s) 15:06, Elvis Martis <elvis_bcp.elvismartis.in> escribió:
>
> The command looks ok to me
> However, there is a problem in the mmpbsa.in. Look at this one I edited for
> you.
>
> &general
> interval=1, netcdf=1,
> keep_files=0,
> /
> &gb
> igb=8,
> saltcon=0.0, surften=0.0072,
> surfoff=0.0, molsurf=0,
> /
> &nmode
> drms=0.001, maxcyc=10000,
> nminterval=5000, nmendframe=10000,
> nmode_igb=1,
> /
>
> Best Regards
> Elvis
>
>
>
>> On Mon, 24 Aug 2020 at 23:27, Camila Clemente <camilamaraclemente.gmail.com>
>> wrote:
>>
>> Hi Elvis!
>>
>> When I put:
>> $AMBERHOME/bin/MMPBSA.py -O -i mmgbsa.in -o r_500_prod1.mmgbsa.results.dat
>> -eo r_500_prod1.mmgbsa.per-frame.dat \
>> -sp r_500.wet.complex.prmtop -cp r_500.gas.complex.prmtop -rp
>> r_500.gas.receptor.prmtop -lp r_500_aux.gas.ligand.prmtop -y
>> r_500_prod1.nc
>>
>> I have a error-log:
>> InputError: Invalid input. Terminate each namelist prior to starting
>> another one.
>> Enter `MMPBSA.py --help` for help
>>
>> the mmgbsa.in is:
>> mmgbsa r_500 analysis
>> &general
>> interval=1, netcdf=1,
>> keep_files=0,
>>
>> &gb
>> igb=8,
>> saltcon=0.0, surften=0.0072,
>> surfoff=0.0, molsurf=0,
>>
>> &nmode
>> drms=0.001, maxcyc=10000,
>> nminterval=5000, nmendframe=10000,
>> nmode_igb=1,
>> /
>>
>> Do you now the mistake?
>>
>> When I try with the tutorial amber with .mdcrd i do not have problem
>>
>>
>> El lun., 24 ago. 2020 a las 14:50, Elvis Martis (<elvis_bcp.elvismartis.in
>>> )
>> escribió:
>>
>>> Yes!
>>> That is a valid format.
>>> Best Regards
>>> Elvis
>>>
>>>
>>>
>>> On Mon, 24 Aug 2020 at 23:11, Camila Mara Clemente <
>>> camilamaraclemente.gmail.com> wrote:
>>>
>>>> Hi
>>>>
>>>> Can I use my trajectories in format .nc in MMPBSA.py?
>>>>
>>>> Thank you
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>> --
>> *Camila*
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Mon Aug 24 2020 - 11:30:03 PDT
