[AMBER] error with restraint distance minimization

From: Michael Shokhen <michael.shokhen.biu.ac.il>
Date: Wed, 25 Oct 2017 16:02:52 +0000

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 <http://min1.in> -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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Received on Wed Oct 25 2017 - 09:30:03 PDT
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