Hello Renato,
I have faced a similar error on protein minimizations especially if the system is energetically unfavourable conformation.
But first, I would set ntpr=1, see the output at each small step and see at what NSTEP does the segfault happen.
Lastly I sometimes have to play with the tolerance value (see tol=0.0001) That helps at times.
Lastly you may need to put restraint on the protein backbone and slowly release the restrain weight from 10 to 8 to 5 to 2 .. then finally bring it to unrestrained minimization.
Thanks
Debarati
From: Renato Araujo<mailto:renatoacufpa.gmail.com>
Sent: 23 June 2020 15:06
To: AMBER Mailing List<mailto:amber.ambermd.org>
Subject: [AMBER] Minimization erro
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 Pará - IFPA
Grupo de Modelagem Molecular - UFPA
Tel.+55 91 985484622
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Received on Tue Jun 23 2020 - 16:00:03 PDT
