Dear all
I am trying to perform a "belly dynamics" MD run.Below is my output
file. As you can see it crashes after reading in the "belly residues".Can
anyone see where I'm going wrong. I'm a new user so it may be something
obvious. Thanks in advance for any responce.
All the Best, Eoin Galligan
-------------------------------------------------------
Amber 5 SANDER Scripps/UCSF 1997
-------------------------------------------------------
| Run at 10:50:14 on 13 day of
month 12, 19 0
[-O]verwriting output
File Assignments:
|MDIN : mdtest-input.in
|MDOUT: mdtest-output.out
nrun=10,nstlim=500,ntcm=1,nscm=100,init=4,dt=0.002,
temp0=300.0,ntt=5,
ntp=0,ntc=3,
iftres=1,
nmropt=1,
&end
-- belly
RES 1 63
RES 68 68
RES 70 70
RES 72 74
RES 82 82
RES 92 107
RES 109 129
RES 131 131
RES 133 133
RES 138 147
RES 150 159
RES 163 381
END
END
&wt
type= 'END'
&end
&rst
iat = 1690,2590,
r1=50.31,r2=52.51,r3=52.51,r4=54.71,
rk2=100, rk3=100,
&end
-------------------------------------------------------------------------------
n ps restrained md on dhfr mtx system
| Reading &cntrl namelist w/ portable lib
1. RESOURCE USE:
NATOM = 3265 NTYPES = 16 NBONH = 1935 MBONA = 1367
NTHETH = 2907 MTHETA = 1865 NPHIH = 5274 MPHIA = 3418
NHPARM = 0 NPARM = 0 NNB = 15288 NRES = 381
NBONA = 1367 NTHETA = 1865 NPHIA = 3418 NUMBND = 52
NUMANG = 113 NPTRA = 37 NATYP = 33 NPHB = 1
IFBOX = 0 NMXRS = 54 IFCAP = 1
| Memory type Allocated
| Real 117645
| Hollerith 26503
| Integer 208008 (static)
| Max Nonbonded Pairs: 3346506 packed 2 to a machine word
cap option on:
NATCAP = 2611 CUTCAP = 20.000 XYZCAP = 132.063 0.926 3.633
2. CONTROL DATA FOR THE RUN
TIMLIM= 999999. IREST = 1 IBELLY= 1
KFORM = 1 ICHDNA= 0 IMIN = 0
IPOL = 0 IEWALD= 0
NTX = 7 NTXO = 1
IG = 71277 TEMPI = 0.00 HEAT = 0.000
NTB = 0 IFTRES= 1 BOXX = 0.000
BOXY = 0.000 BOXZ = 0.000
NRUN = 10 NTT = 5 TEMP0 = 300.000
DTEMP = 0.000 TAUTP = 0.200 TAUTS = 0.200
ISOLVP= 0 VLIMIT= 0.000
NTP = 0 PRES0 = 1.000 COMP = 44.600
TAUP = 0.200 NPSCAL= 0
NTCM = 0 NSCM = 9999999
NSTLIM= 500 INIT = 4 NTU = 1
T = 0.000 DT = 0.00200
NTC = 3 TOL = 0.00050 JFASTW = 0
NTF = 3 NTID = 0 NTNB = 1
NSNB = 25 IDIEL = 1 IMGSLT= 0
IPRR = 0 IPRW = 0 ITRSLU= 1
CUT = 15.000 SCNB = 2.000
SCEE = 1.200 DIELC = 1.000
CUT2ND= 0.00000
NTPR = 50 NTWR = 50 NTWX = 500
NTWV = 0 NTWE = 500 NTWXM = 999999
NTWVM = 999999 NTWEM = 999999 IOUTFM= 0
NTWPRT= 0 NTWPR0= 0
NTR = 0 NTRX = 1
TAUR = 0.00000 NMROPT= 1 ISFTRP= 0
RWELL = 1.00000 PENCUT= 0.10000
IVCAP = 0 MATCAP= 0 FCAP = 1.500
OTHER DATA:
IFCAP = 1 NATCAP= 2611 CUTCAP= 20.000
XCAP = 132.063 YCAP = 0.926 ZCAP = 3.633
NATOM = 3265 NRES = 381
Water definition for fast triangulated model:
Resname = WAT ; Oxygen_name = O ; Hyd1_name = H1 ; Hyd2_name = H2
LOADING THE BELLY ATOMS AS GROUPS
tel: 0115 9515151 ext 66272
mobile: 07968 349629
mobile email: eoingalligan_at_sms.genie.co.uk
(160 char max)
Laboratory of Biophysics and Surface Analysis,
Institute of Pharmaceutical Sciences,
Nottingham University,
University Park,
Nottingham,
NG7 2RD,
UK
Received on Wed Dec 13 2000 - 09:12:51 PST
