we can't know for sure without more detail, but if you use ntc=1 then you
should also use ntf=1.
On Wed, Aug 30, 2023 at 9:00 AM KAJAL ABROL via AMBER <amber.ambermd.org>
wrote:
> 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
> ReplyForward
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Received on Wed Aug 30 2023 - 06:30:02 PDT
