Dear AMBER community,
I am facing issue in running energy minimization of a protein system in
AMBER. I am using the following script to run the energy minimization
step:
minimization of solvent
&cntrl
imin = 1, maxcyc = 1000,
ncyc = 20, ntx = 1,
ntwe = 0, ntwr = 500, ntpr = 50,
ntc = 1, ntf = 2, ntb = 1, ntp = 0,
cut = 10.0,
ntr=1, restraintmask = ':1-180'
restraint_wt = 100.,
ioutfm=1, ntxo=2,
/
*Command: *$AMBERHOME/bin/sander -O -i 1min.in -o 1min.out -p solv.top -c
solv.crd -r 1min.rst7 -inf 1min.info -ref solv.crd -x mdcrd.1min
*Error:* Program received signal SIGSEGV: Segmentation fault - invalid
memory reference.
Backtrace for this error:
#0 0x7fa6702a0d11 in ???
#1 0x7fa67029fee5 in ???
#2 0x7fa6700b608f in ???
at
/build/glibc-SzIz7B/glibc-2.31/signal/../sysdeps/unix/sysv/linux/x86_64/sigaction.c:0
#3 0x557d0d082862 in ???
#4 0x557d0d084f08 in ???
#5 0x557d0cfc0d80 in ???
#6 0x557d0d01b82b in ???
#7 0x557d0d006223 in ???
#8 0x557d0cfff05c in ???
#9 0x557d0cfff0b8 in ???
#10 0x7fa670097082 in __libc_start_main
at ../csu/libc-start.c:308
#11 0x557d0ce32ded in ???
#12 0xffffffffffffffff in ???
Segmentation fault (core dumped)
*The output file is showing:* It is running till 150 NSTEP and then it is
showing ... RESTARTED DUE TO LINMIN FAILURE ...
NSTEP ENERGY RMS GMAX NAME NUMBER
50 -3.8361E+04 1.8400E+01 7.9952E+02 OE1 3081
BOND = 1426.9490 ANGLE = 2586.2280 DIHED =
2968.7530
VDWAALS = -5510.2852 EEL = -59369.0190 HBOND =
0.0000
1-4 VDW = 2896.8618 1-4 EEL = 14460.4525 RESTRAINT =
1802.9163
CMAP = 376.4567
EAMBER = -40163.6033
NSTEP ENERGY RMS GMAX NAME NUMBER
100 -4.5804E+04 1.0018E+02 1.5049E+04 OE1 3081
BOND = 554.7705 ANGLE = 1813.6795 DIHED =
2839.1250
VDWAALS = -5899.2642 EEL = -64423.5807 HBOND =
0.0000
1-4 VDW = 2915.5867 1-4 EEL = 14601.0029 RESTRAINT =
1411.5788
CMAP = 383.5965
EAMBER = -47215.0839
NSTEP ENERGY RMS GMAX NAME NUMBER
150 -8.6234E+04 5.2917E+04 6.5474E+06 OE2 5883
BOND = 824.4216 ANGLE = 1842.1523 DIHED =
2824.8736
VDWAALS = -5916.9259 EEL = -105506.7943 HBOND =
0.0000
1-4 VDW = 2901.6148 1-4 EEL = 14587.7345 RESTRAINT =
1822.9481
CMAP = 385.7165
EAMBER = -88057.2069
... RESTARTED DUE TO LINMIN FAILURE ...
*Please suggest me any solution for rectifying this error. *
Thanks and Regards,
Kajal Abrol
Research Scholar
Department of Bioinformatics
Pondicherry University
Puducherry
India
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Received on Wed Aug 30 2023 - 06:30:02 PDT
