Here are my command, I think they aren't right ?
In fact it doesn't do any error but don't produce the expected files ...
sander -O -i mini.in -o mini.out -p dna.prmtop -c dna.rst7 -r mini.rst
-ref dna.rst7
sander -O -i heat.in -o heat.out -p dna.prmtop -c mini.rst -r heat.rst
-x heat.mdcrd -ref mini.rst
sander -O -i eq.in -o eq.out -p dna.prmtop -c heat.rst -r eq.rst -x
eq.mdcrd -ref heat.rst
sander -O -i md.in -o md.out -p dna.prmtop -c eq.rst -r md.rst7 -x md.nc
-inf mdinfo
and all the files i have in the directory :
A-dna.pdb dna.prmtop dna.rst7 eq.in eq.out heat.in heat.out
leap.log md.in md.out mini.in mini.out
But it should generate md.rst7 and a md.nc (obviously not created )
Best regards
Henri
On 01/10/2020 19:29, Elvis Martis wrote:
> You could use sander instead of pmemd.
> But sander won't run on GPUs
> Best Regards
> Elvis
>
>
>
> On Thu, 1 Oct 2020 at 22:45, aishen <aishen.free.fr
> <mailto:aishen.free.fr>> wrote:
>
> I compiled amber20_src then you are saying I don't have pmemd,
> very strange ... I think I won't use any more this soft
>
> Best regards and thank you for the answer
>
> Henri
>
> On 01/10/2020 19:02, Elvis Martis wrote:
>> If you did not build amber then you will not find pmemd.
>> pmemd is paid code of amber.
>> Best Regards
>> Elvis
>>
>>
>>
>> On Thu, 1 Oct 2020 at 22:30, aishen <aishen.free.fr
>> <mailto:aishen.free.fr>> wrote:
>>
>> I thaught too but it's not maybe it wasn't build ? could it be ?
>>
>> On 01/10/2020 18:49, Elvis Martis wrote:
>> > Typing "which pmemd" should echo its path.
>> > It is general in $AMBERHOME/bin
>> > Best Regards
>> > Elvis
>> >
>> >
>> >
>> > On Thu, 1 Oct 2020 at 22:18, aishen <aishen.free.fr
>> <mailto:aishen.free.fr>> wrote:
>> >
>> >> Hi,
>> >>
>> >> I am trying to do this tutorial but I can't find pmemd
>> where is this
>> >> programm from ?
>> >>
>> >>
>> https://amberhub.chpc.utah.edu/analisis-of-nucleic-acid-simulation/
>> >>
>> >> Any help
>> >>
>> >> Regards
>> >>
>> >> Henri
>> >>
>> >>
>> >>
>> >> _______________________________________________
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>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >>
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>>
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Received on Thu Oct 01 2020 - 14:00:03 PDT
