[hisano]

Dear all,

I tried to run minimization for a protein with membrane bilayer (POPC) generated via the charmm-gui website, but the calculation terminated with an error message:

————————————————————————–
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: [[11717,1],2]
Exit code: 1
————————————————————————–

 

The log stopped with warnings at:

Check_bonding> distance in dihedral is grater than cellsize: 19264 19271 8.90659
rank_no = 1
Check_bonding> distance in dihedral is grater than cellsize: 14842 14849 9.29054
rank_no = 2
WARNING: too long bond: 9558 9561 2.04024
WARNING: too long bond: 14588 14591 2.25202
WARNING: too long bond: 14591 14594 2.03494
WARNING: too long bond: 18643 18646 2.49956
WARNING: too long bond: 5812 5815 2.04813
WARNING: too long bond: 8443 8446 3.16633
WARNING: too long bond: 8437 8440 2.17867
WARNING: too long bond: 9643 9646 3.05041
WARNING: too short bond: 9646 9649 0.91778
Setup_Fitting_Spdyn> NO fitting is applied, skip
fitting method = NO

 

How can I solve this problem?

 

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[hisano]

If I used step6.0_minimization.dihe (included in the charmm-gui downloaded files) as a localresfile input, the job run normally (or at least the problem above was solved). However, another question is raised against this procedure. The tutorial2022 (session 6.1) says “However, in this tutorial, we will use a slightly modified version of these files to take advantage of GENESIS 2.0 latest features”, and used a restraint file which is not the one downloaded from charmm-gui. If this is also true for the session 6.2, how can I get a restraint file for the GENESIS 2.0?

[jwjung]

To solve the problem, the easiest solution is to increase the cell size. You can increase the cell size by assigning larger pairlistdist values. Could you increase it gradually up to 17 and run it? If minimization is done well, you can use the original pairlistdist values from the next run.