[AMBER] pH-REMD error

From: Kolattukudy P. Santo <santotheophys.gmail.com> Date: Sun, 21 Jun 2020 12:35:12 -0400

--
Launching AMBER's PMEMD (Particle Mesh Ewald Molecular Dynamics):
 Checking cpin file and/or cein file.
 We are going to find DELTAGREF for a pH titratable residue using Replica
Exchange.
 The solvent pH value of replica    1 is   2.000 and was loaded from the
mdin file (pH2/md1.in).
 The solvent pH value of replica    2 is   2.500 and was loaded from the
mdin file (pH25/md1.in).
 The solvent pH value of replica    3 is   3.000 and was loaded from the
mdin file (pH3/md1.in).
 The solvent pH value of replica    4 is   3.500 and was loaded from the
mdin file (pH35/md1.in).
 The solvent pH value of replica    5 is   4.000 and was loaded from the
mdin file (pH4/md1.in).
 The target pKa is    3.21000.
 The temperature is   300.00 K and was loaded from the mdin file (pH2/md1.in
).
 According to the mdin file (pH2/md1.in), the value of ntcnstph is 5.
 According to the mdin file (pH2/md1.in), the value of nstlim is 100.
 According to the mdin file (pH2/md1.in), the value of numexchg is 5000.
 The program will try to find a range of values for DELTAGREF
automatically, as the argument -dgrefrange was not given
 AMBER execution #1: running 5000 MD steps (50 replica exchange attempts)
for DELTAGREF = 0.000000 kcal/mol
ERROR: The execution of AMBER using the binary
/projects/community/gcc/5.4/mvapich2/2.2/cuda/9.0/amber/18/kholodvl/bin/pmemd.MPI
failed. The execution returned the following STDERR:
       slurmstepd: error: *** STEP 37153230.0 ON gpu006 CANCELLED AT
2020-06-21T12:20:32 ***
       The command executed was:
       srun --kill-on-bad-exit  -n 5  --mpi=pmi2
/projects/community/gcc/5.4/mvapich2/2.2/cuda/9.0/amber/18/kholodvl/bin/pmemd.MPI
-ng 5 -groupfile groupfile.temporary
       Check the mdout file (pH2/md1.out) to see what the error might be.
Also check if all libraries necessary to run AMBER are properly set.
       The execution of finddgref.py stopped
  NTasks     MaxRSS  MaxVMSize     AveRSS  AveVMSize     AveCPU    Elapsed
-------- ---------- ---------- ---------- ---------- ---------- ----------
                                                                  00:00:14
       1                                                          00:00:14
       5      1664K    352260K    1700659    352260K   00:00:00   00:00:01
--------------------
No PH2/md1.out was created. What could be the error here ?
-- 
Best,
KP Santo
--------------------------------------------------------------
Dr. Kolattukudy P.  Santo
Post doctoral Associate
Department of Chemical and Biochemical Engineering
Rutgers, The State University of New Jersey
New Brunswick, New jersey
USA
---------------------------------------------------------
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