[AMBER] Minimization erro

From: Renato Araujo <renatoacufpa.gmail.com>
Date: Tue, 23 Jun 2020 16:05:59 -0300

Hello everyone

I'm doing four minimization steps as follows:
In the first, you specify the water and ion residues (cl- or Na +).
In the second, only the protein residues (H minimization);
In the third, it specifies protein + water (Leaving ions out).
The last is a general minimization, I don't specify anything.

The first three steps occur without errors, but the last one gives this
messages in the terminal:

Program received signal SIGSEGV: Segmentation fault - invalid memory
reference.

Backtrace for this error:

Program received signal SIGSEGV: Segmentation fault - invalid memory
reference.

Backtrace for this error:
#0 0x7f53f713732a
#1 0x7f53f7136503
#2 0x7f53f6594f1f
#3 0x561510ec46e8
#4 0x561510ec6798
#5 0x561511138083
#6 0x561510e36c45
#7 0x561510e2ca88
#8 0x561510e2cb6b
#9 0x7f53f6577b96
#10 0x561510da5669
#11 0xffffffffffffffff
#0 0x7f0e812e232a
#1 0x7f0e812e1503
#2 0x7f0e8073ff1f
#3 0x5578bfc666e8
#4 0x5578bfc68798
#5 0x5578bfeda083
#6 0x5578bfbd8c45
#7 0x5578bfbcea88
#8 0x5578bfbceb6b
#9 0x7f0e80722b96
#10 0x5578bfb47669
#11 0xffffffffffffffff
--------------------------------------------------------------------------
mpirun noticed that process rank 1 with PID 0 on node renato exited on
signal 11 (Segmentation fault).
My output is as follows:


          -------------------------------------------------------
          Amber 18 SANDER 2018
          -------------------------------------------------------

| Run on 06/23/2020 at 11:26:48

| Executable path: sander.MPI
| Working directory: /home/renato/Documentos/DM_dengue/lig_13f/min
| Hostname: Unknown
  [-O]verwriting output

File Assignments:
| MDIN: mdin_min4

| MDOUT: min4.out

|INPCRD: min3.rst

| PARM: complex_solv.prmtop

|RESTRT: min4.rst

| REFC: refc

| MDVEL: mdvel

| MDFRC: mdfrc

| MDEN: mden

| MDCRD: mdcrd

|MDINFO: mdinfo

| MTMD: mtmd

|INPDIP: inpdip

|RSTDIP: rstdip

|INPTRA: inptraj


| REMLOG: rem.log
| REMTYPE: rem.type
| REMSTRIP:
| SAVEENE: saveene
|CLUSTERINF: cluster.info
| RESERVOIR: reserv/frame
| REMDDIM:


 Here is the input file:

Mnimization ALL

&cntrl

 imin=1, ntx=1,

 ntpr=1000, ntwr=5000, ibelly=0,

 maxcyc=10000, ncyc=5000,

&end


--------------------------------------------------------------------------------
   1. RESOURCE USE:
--------------------------------------------------------------------------------

| Flags: MPI

 getting box info from netcdf restart file
| NetCDF restart box info found
|Largest sphere to fit in unit cell has radius = 31.401
| New format PARM file being parsed.
| Version = 1.000 Date = 06/22/20 Time = 20:44:52
 NATOM = 30381 NTYPES = 20 NBONH = 28301 MBONA = 2114
 NTHETH = 4753 MTHETA = 2854 NPHIH = 9600 MPHIA = 8877
 NHPARM = 0 NPARM = 0 NNB = 57930 NRES = 9008
 NBONA = 2114 NTHETA = 2854 NPHIA = 8877 NUMBND = 94
 NUMANG = 208 NPTRA = 213 NATYP = 54 NPHB = 1
 IFBOX = 2 NMXRS = 40 IFCAP = 0 NEXTRA = 0
 NCOPY = 0


| Memory Use Allocated
| Real 2549560
| Hollerith 100153
| Integer 1599490
| Max Pairs 1265875
| nblistReal 364572
| nblist Int 1126788
| Total 38752 kbytes

| Note: 1-4 EEL scale factors are being read from the topology file.

| Note: 1-4 VDW scale factors are being read from the topology file.
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals

     BOX TYPE: TRUNCATED OCTAHEDRON

--------------------------------------------------------------------------------
   2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------

default_name


General flags:
     imin = 1, nmropt = 0

Nature and format of input:
     ntx = 1, irest = 0, ntrx = 1

Nature and format of output:
     ntxo = 2, ntpr = 1000, ntrx = 1, ntwr =
 5000
     iwrap = 0, ntwx = 0, ntwv = 0, ntwe =
  0
     ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat=
   0

Potential function:
     ntf = 1, ntb = 1, igb = 0, nsnb =
 25
     ipol = 0, gbsa = 0, iesp = 0
     dielc = 1.00000, cut = 8.00000, intdiel = 1.00000

Frozen or restrained atoms:
     ibelly = 0, ntr = 0

Energy minimization:
     maxcyc = 10000, ncyc = 5000, ntmin = 1
     dx0 = 0.01000, drms = 0.00010

Ewald parameters:
     verbose = 0, ew_type = 0, nbflag = 1, use_pme =
  1
     vdwmeth = 1, eedmeth = 1, netfrc = 0
     Box X = 76.918 Box Y = 76.918 Box Z = 76.918
     Alpha = 109.471 Beta = 109.471 Gamma = 109.471
     NFFT1 = 80 NFFT2 = 80 NFFT3 = 80
     Cutoff= 8.000 Tol =0.100E-04
     Ewald Coefficient = 0.34864
     Interpolation order = 4

| MPI Timing options:
| profile_mpi = 0
| INFO: Old style inpcrd file read


--------------------------------------------------------------------------------
   3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------

default_name

 begin time read from input coords = 0.000 ps

 Number of triangulated 3-point waters found: 8738
| Atom division among processors:
| 0 3798 7596 11391 15189 18987 22782 26580
| 30381

     Sum of charges from parm topology file = -0.00000008
     Forcing neutrality...
| Running AMBER/MPI version on 8 nodes


--------------------------------------------------------------------------------
   4. RESULTS
--------------------------------------------------------------------------------

 ---------------------------------------------------
 APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
 using 5000.0 points per unit in tabled values
 TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960
 ---------------------------------------------------
| Local SIZE OF NONBOND LIST = 698087
| TOTAL SIZE OF NONBOND LIST = 5569574


   NSTEP ENERGY RMS GMAX NAME NUMBER
      1 -1.2016E+05 3.1238E+00 1.9733E+02 CD 228

 BOND = 9200.9187 ANGLE = 618.0340 DIHED =
3006.4760
 VDWAALS = 21690.8594 EEL = -165137.8675 HBOND =
 0.0000
 1-4 VDW = 1049.7757 1-4 EEL = 9412.6505 RESTRAINT =
 0.0000


   NSTEP ENERGY RMS GMAX NAME NUMBER
   1000 -4.9483E+07 9.5761E+10 1.4210E+13 H 4117

 BOND = 9379.9938 ANGLE = 591.6063 DIHED =
2912.8623
 VDWAALS = 21737.5492 EEL = ************* HBOND =
 0.0000
 1-4 VDW = 827.5770 1-4 EEL = 8939.7758 RESTRAINT =
 0.0000


   NSTEP ENERGY RMS GMAX NAME NUMBER
   2000 -1.9546E+08 1.4996E+12 2.2252E+14 H 4117

 BOND = 9379.9933 ANGLE = 591.6063 DIHED =
2912.8623
 VDWAALS = 21737.5484 EEL = ************* HBOND =
 0.0000
 1-4 VDW = 827.5770 1-4 EEL = 8939.7758 RESTRAINT =
 0.0000


   NSTEP ENERGY RMS GMAX NAME NUMBER
   3000 -1.2560E+08 6.1884E+11 9.1827E+13 H 4117

 BOND = 9379.9934 ANGLE = 591.6063 DIHED =
2912.8623
 VDWAALS = 21737.5485 EEL = ************* HBOND =
 0.0000
 1-4 VDW = 827.5770 1-4 EEL = 8939.7758 RESTRAINT =
 0.0000


   NSTEP ENERGY RMS GMAX NAME NUMBER
   4000 -4.9483E+07 9.5761E+10 1.4210E+13 H 4117

 BOND = 9379.9938 ANGLE = 591.6063 DIHED =
2912.8623
 VDWAALS = 21737.5492 EEL = ************* HBOND =
 0.0000
 1-4 VDW = 827.5770 1-4 EEL = 8939.7758 RESTRAINT =
 0.0000


   NSTEP ENERGY RMS GMAX NAME NUMBER
   5000 -1.9546E+08 1.4996E+12 2.2252E+14 H 4117

 BOND = 9379.9933 ANGLE = 591.6063 DIHED =
2912.8623
 VDWAALS = 21737.5484 EEL = ************* HBOND =
 0.0000
 1-4 VDW = 827.5770 1-4 EEL = 8939.7758 RESTRAINT =
 0.0000


please suggestions for this error

thank you
-- 
Prof Dr Renato Costa
Instituto Federal do ParĂ¡ - IFPA
Grupo de Modelagem Molecular - UFPA
Tel.+55  91 985484622
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Received on Tue Jun 23 2020 - 12:30:03 PDT
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