Michael:
same advice we have given you several times:
That error does not tell us anything at all, it could happen for many
several reasons.
For starters, make sure all the input files, etc are in the directory
pmemd thinks they are in, change ntpr to 1 so you print every step, etc.
adrian
On 10/25/17 12:02 PM, Michael Shokhen wrote:
> Dear Amber experts,
>
>
> I need to conduct restraint minimization by Amber16 with ff14SB force field
>
> of my protein with restraint disulfide bond distances.
>
>
> System reports an error:
>
> STOP PMEMD Terminated Abnormally!
>
>
> Below is the command running minimization and
>
> the corresponding input files.
>
> Please show me where is my error and what should be
>
> the correct variant.
>
>
> Thank you,
>
> Michael
>
>
> command:
>
>
> pmemd.cuda -O -i min1.in <https://urldefense.proofpoint.com/v2/url?u=http-3A__min1.in&d=DwICAg&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=JAg-KQEjdZeg_E8PHDDoaw&m=9v3SH9eliTNzsSnYL4n73J4JdJ2gZz4FDBSgJWFYlw0&s=kytZInrIlrkrN2jfTRNtveLxRWFQ2L6unLPKG0rcwWU&e= > -o min1.out -p ../mc.prmtop -c ../mc.inpcrd -r mc_min1.rst -ref ../mc.inpcrd &
>
>
> min1.in script:
>
>
> System minimization:
> &cntrl
> imin=1, ntmin=1, nmropt=0, drms=0.1
> maxcyc=20000, ncyc=1500,
> ntx=1, irest=0,
> ntpr=100, ntwr=100, iwrap=0,
> ntf=1, ntb=1, cut=10.0, nsnb=20,
> igb=0,
> ibelly=0, ntr=1, nmropt=1,
> &end
> &wt
> type='END',
> &end
> DISANG = rst_disulf.dist
>
>
> rst_disulf.dist input file:
>
> #
> # CYS_31 - CYS_47: S-S distance = 2.038448 Ang.
> &rst
> ixpk= 0, nxpk= 0, iat= 447, 687, r1= 1.70, r2= 2.0, r3= 2.2, r4= 2.3,
> rk2=0.0, rk3=70.0, ir6=1, ialtd=0,
> &end
> #
> # CYS_128 - CYS_195: S-S distance = 2.043326 Ang.
> &rst
> ixpk= 0, nxpk= 0, iat= 1934, 2872, r1= 1.70, r2= 2.0, r3= 2.2, r4= 2.3, &end
> #
> # CYS_159 - CYS_175: S-S distance = 2.033610 Ang.
> &rst
> ixpk= 0, nxpk= 0, iat= 2414, 2641, r1= 1.70, r2= 2.0, r3= 2.2, r4= 2.3, &end
> #
> # CYS_185 - CYS_215: S-S distance = 2.030679 Ang.
> &rst
> ixpk= 0, nxpk= 0, iat= 2752, 3164, r1= 1.70, r2= 2.0, r3= 2.2, r4= 2.3, &end
> #
> # CYS_248 - CYS_277: S-S distance = 2.024516 Ang.
> &rst
> ixpk= 0, nxpk= 0, iat= 3670, 4123, r1= 1.70, r2= 2.0, r3= 2.2, r4= 2.3, &end
> #
> # CYS_255 - CYS_281: S-S distance = 2.034776 Ang.
> &rst
> ixpk= 0, nxpk= 0, iat= 3794, 4166, r1= 1.70, r2= 2.0, r3= 2.2, r4= 2.3, &end
> #
> # CYS_264 - CYS_276: S-S distance = 2.061528 Ang.
> &rst
> ixpk= 0, nxpk= 0, iat= 3930, 4113, r1= 1.70, r2= 2.0, r3= 2.2, r4= 2.3, &end
> #
> # CYS_270 - CYS_285: S-S distance = 2.025572 Ang.
> &rst
> ixpk= 0, nxpk= 0, iat= 4019, 4210, r1= 1.70, r2= 2.0, r3= 2.2, r4= 2.3, &end
> #
>
>
>
>
>
>
>
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--
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Wed Oct 25 2017 - 09:30:05 PDT
