Hello, I tried a minimization in Sander and got this output:
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Amber 7 SANDER Scripps/UCSF 2002
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| Run on Mon Apr 14 17:27:43 1952
[-O]verwriting output
File Assignments:
| MDIN: /work/miranda/pidimer_min.in
| MDOUT: /work/miranda/pidimer_min.out
|INPCRD: /work/miranda/pidimer.inpcrd
| PARM: /work/miranda/pidimer.prmtop
|RESTRT: /work/miranda/pidimer.mincrd
| REFC: /work/miranda/pidimer.inpcrd
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: /work/miranda/pidimer_min.info
|INPDIP: inpdip
|RSTDIP: rstdip
Here is the input file:
&cntrl
igb = 0, ntb = 1, ntpr = 50,
cut = 9.0,
ibelly = 0, ntr = 0,
imin = 1, maxcyc = 1000, ncyc = 1000,
&end
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1. RESOURCE USE:
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| Flags: MEM_ALLOC MPI RLE ROWAT
getting new box info from bottom of inpcrd
| peek_ewald_inpcrd: Box info found
| New format PARM file being parsed.
| Version = 1.000 Date = 06/28/03 Time = 12:54:43
NATOM = 84809 NTYPES = 19 NBONH = 77456 MBONA = 7516
NTHETH = 16478 MTHETA = 10174 NPHIH = 29868 MPHIA = 17886
NHPARM = 0 NPARM = 0 NNB = 174347 NRES = 24329
NBONA = 7516 NTHETA = 10174 NPHIA = 17886 NUMBND = 48
NUMANG = 96 NPTRA = 34 NATYP = 34 NPHB = 1
IFBOX = 1 NMXRS = 24 IFCAP = 0 NEXTRA = 0
| Memory Use Allocated
| Real 6818828
| Hollerith 533185
| Integer 5252296
| Max Pairs 4031456
| Max Rstack 2000000
| Max Istack 2000000
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
BOX TYPE: RECTILINEAR
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2. CONTROL DATA FOR THE RUN
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General flags:
imin = 1, nmropt = 0
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500
iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0
ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function:
ntf = 1, ntb = 1, igb = 0, nsnb = 25
ipol = 0, gbsa = 0
dielc = 1.00000, cut = 9.00000, intdiel = 1.00000
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Energy minimization:
maxcyc = 1000, ncyc = 1000, ntmin = 1
dx0 = 0.01000, dxm = 0.50000, drms = 0.00010
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
vdwmeth = 1, eedmeth = 1, frc_int = 0, netfrc = 1
Box X = 95.869 Box Y = 112.893 Box Z = 99.514
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 96 NFFT2 = 120 NFFT3 = 100
Cutoff= 9.000 Tol =0.100E-04
Ewald Coefficient = 0.30768
Interpolation order = 4
| PLEVEL = 1: runmd parallelization, no EKCMR
Exceeding lastist in get_istack
lastist = 2000000
top_stk= 1950607
isize = 84809
request= 2035416
Increase lastist in the &cntrl namelist
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For what I understand, there is a problem with the value called lastist, but I
don't know what that means. Could someone help me with this please? Thank you.
Received on Sat Jun 28 2003 - 14:53:01 PDT
