Hi,
The fact that cpptraj's output stops during the Action setup phase
indeed indicates some error occurred with cpptraj. Were there any
other error messages written? The ones from cpptraj just start with
'Error:'.
-Dan
PS - @mmpbsa.py devs: Is stderr from cpptraj captured by mmpbsa.py and
directed somewhere?
On Sat, Sep 9, 2017 at 11:55 PM, Nada Afiva <nadaafiva.gmail.com> wrote:
> Dear Prof. Hay,
> Attached is "_MMPBSA_cpptraj_entropy.out" file.
> The command for performing quasiharmonic calculation:
> mpirun -np 6 MMPBSA.py.MPI -i nmode.in -cp com.prmtop -rp rec.prmtop -lp
> lig.prmtop -y prod.binpos
>
> For information, I performed MD production of the system contained solvated
> receptor (protein, DNA, MG ions) and ligand.
> And before performing quasiharmonic, I stript out all solvent and MG and
> Na+ ions.
>
> Thanks for your response.
>
> Best!
> nadaafiva
>
> On Sun, Sep 10, 2017 at 10:52 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>
>> detail commands + output would be really helpful. cheers
>> Hai
>>
>> On Sat, Sep 9, 2017 at 10:50 PM, Nada Afiva <nadaafiva.gmail.com> wrote:
>>
>> > Dear all,
>> >
>> > I am performing quasiharmonic calculation for receptor-ligand complex.
>> The
>> > receptor contains protein, DNA, and MG ions.
>> >
>> > My input file was:
>> >
>> >
>> > Input file
>> >
>> > &general
>> >
>> > Startframe=15000, endframe=20000, interval=500,
>> >
>> > Keep_files=2, entropy-1,
>> >
>> > /
>> >
>> >
>> >
>> > However, the calculation always failed with error “CalcError:
>> > /home/amber16/bin/cpptraj failed with prmtop protein-ligand.prmtop!
>> >
>> > The error seems to be due to prmtop file, but I have performed entalphy
>> > calculation using MMPBSA.py with the same prmtop file, and it run
>> > successfully.
>> >
>> > So I am wondering how to solve that problem.
>> >
>> > Thansk so much for any comment suggestion.
>> >
>> >
>> >
>> > Best!
>> >
>> > nadaafiva
>> > _______________________________________________
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>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Mon Sep 11 2017 - 09:30:02 PDT
