Dear Professor,
Thank you a lot for your reply. Following your suggestion, I tried the command;
$ cpptraj -p complex.prmtop -y complex.nc -tl
Frames: 151021
Maybe, it tells the trajectory file is OK. I looked for the variables of total frames in the python script. In the make_trajs.py I find these lines;
framere = re.compile(r'Frames: (\d+)')
...
for traj in self.traj_files:
process = Popen([self.exe, '-p', str(self.prmtop), '-y', traj, '-tl'],
stdin=PIPE, stdout=PIPE)
...
output = output.decode()
...
num_frames = framere.findall(output)
I have given up to find the causes of this error. It seems to result something in the operating system or python engine. I decide to trim the trajectory for MM-PBSA.py with cpptraj.
Thank you so much for your advice.
Sincerely
Yuji Okabe
2018年6月11日 21:03, "David A Case" <david.case.rutgers.edu> wrote:
> On Mon, Jun 11, 2018, 岡部 勇二 wrote:
>
>> TrajError: start frame (51021) > total frames (5000)
>>
>> Here is my batch file for cpptraj to make the long trajectory;
>>
>> parm solution.prmtop
>> trajin heat.nc
>> trajin equil.nc
>> trajin prod-1.nc
>
> ...
>
>> trajin prod-30.nc
>> trajout complex.nc
>> strip :Na+
>> strip :WAT
>> run
>
> Cpptraj tells you how many frames are in the output trajectory, so it
> would be worth look at that number. Or just run this:
>
> cpptraj -p solution.prmtop -y complex.nc -tl
>
> Which will tell you the number of frames. That will at least eliminate
> one possible source of the problem.
>
> (Also, one would generally not include heating and equilibration steps
> in the trajectory you send to MM-PBSA.)
>
> ...hope this helps....dac
>
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Received on Mon Jun 11 2018 - 07:30:04 PDT
