[nursya]

Hi!

I tried to run Minimization for membrane bilayer of LPS from E. coli Type1 R3, O55(from charmm-gui) as per tutorial. But this error enclosed in Log6.0, thus cannot further proceed to Equilibration.

So how can we solve this?

———————Error in Log6.0———————————————

Select_atom> Syntax error. bracket is not a preliminary rank_no = 0
——————————————————-
Primary job terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
——————————————————-
————————————————————————–
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

Process name: [[4782,1],0]
Exit code: 1

<hr />

While error on Terminal:

ubuntu@ubuntu-VirtualBox:~/Downloads/LPS/genesis$ export OMP_NUM_THREADS=1
ubuntu@ubuntu-VirtualBox:~/Downloads/LPS/genesis$ mpirun -np 1 /home/ubuntu/Downloads/genesis-1.4.0/bin/spdyn step6.0_minimization.inp > log6.0
ubuntu@ubuntu-VirtualBox:~/Downloads/LPS/genesis$ mpirun -np 1 /home/ubuntu/Downloads/genesis-1.4.0/bin/spdyn step6.1_equilibration.inp > log6.1
At line 1480 of file fileio_data.fpp (unit = 7)
Fortran runtime error: Cannot open file ‘step6.0_minimization.rst’: No such file or directory

Error termination. Backtrace:
#0 0x7fcf76fc231a
#1 0x7fcf76fc2ec5
#2 0x7fcf76fc368d
#3 0x7fcf77135c3d
#4 0x7fcf77135f84
#5 0x56390d72b773
#6 0x56390d733c6d
#7 0x56390d7689e1
#8 0x56390d667821
#9 0x56390d700b88
#10 0x56390d705f94
#11 0x56390d4d4ade
#12 0x7fcf763f2b96
#13 0x56390d4d4b09
#14 0xffffffffffffffff

[jwjung]

It seems that you did not write the path of input rst file properly. Could you check if the path of rst file generated from step5 is written correctly in your control input file?

[nursya]

do you mean path input of step5 generated by charmm-gui?

[jwjung]

I checked your log of error again and found that I made a mistake in understanding the errors. You ran step6.0_minimization.inp and step6.1_equilibration.inp, and found errors when running step6.1_equilibration.inp. The error message is that the program could not find the rst file generated from the run of step6.0_minimization. Please check the path of rst file generated from the run of step6.0_minimization, and write the path correctly in step6.1_equilibration.inp. Let us assume  step6.0_minimization.inp and step6.1_equilibration.inp are in directories A and B, respectively, and the rst file from step6.0_minimization exists in A. Then, for example, you need to write “rstfile=../A/step6.0_minimization.rst” in [INPUT] section in step6.1_equilibration.inp.