Dear Amber Developers,
I run MMPBSA.py with the trajectories of inclusion complex of
cyclodexrin. When I use a long trajectory that is combined 32 short
trajectories with cpptraj, I get a following error;
TrajError: start frame (51021) > total frames (5000)
I set the startframe variables 51021 in the input file of MMPBSA.py. The
long trajectory has 151020 frames. The first one of 32 short
trajectories has 20 frames for heating system, the second one has 1000
frames for equilibrating system, and each of the remaining trajectories
have 5000 frames for production MD.
Here is the general namelist variables in my input file;
&general
startframe=51021,
endframe=151020,
interval=20,
verbose=1,
entropy=1,
keep_files=1,
netcdf=1,
/
I wonder the "total frames (5000)" in the error message tell the number
of frames of short productive trajectory. Does trajectory have the
information of the number of frames? If it's right, how do i correct the
information. 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-2.nc
trajin prod-3.nc
trajin prod-4.nc
trajin prod-5.nc
trajin prod-6.nc
trajin prod-7.nc
trajin prod-8.nc
trajin prod-9.nc
trajin prod-10.nc
trajin prod-11.nc
trajin prod-12.nc
trajin prod-13.nc
trajin prod-14.nc
trajin prod-15.nc
trajin prod-16.nc
trajin prod-17.nc
trajin prod-18.nc
trajin prod-19.nc
trajin prod-20.nc
trajin prod-21.nc
trajin prod-22.nc
trajin prod-23.nc
trajin prod-24.nc
trajin prod-25.nc
trajin prod-26.nc
trajin prod-27.nc
trajin prod-28.nc
trajin prod-29.nc
trajin prod-30.nc
trajout complex.nc
strip :Na+
strip :WAT
run
If you think that my orerations or settings caused the error, please
tell me the reason.
Than you in advance for your help.
Yuji Okabe
National Institute of Technology, Miyakonojo College
473-1 Yoshio-cho, Miyakonojo City, Miyazaki Prefecture, JAPAN 885-8567
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Received on Mon Jun 11 2018 - 01:00:02 PDT
