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
