I am attempting to carry out a free energy perturbation with two
mutations in myoglobin with Amber6. The initial state has been
perturbed with the Atom Unit Editor in Leap with appropriate
parameters. The files have been saved via <saveamberparmpert> command.
Here is the resulting gibbs.out file with a terminating error message
<BOX REQUESTED (NTB.ne.0) but no setup in parm>
Not sure where I've gone wrong. Attached is corresponding gibbs.out
file.
Thanks for any help,
Regards,
Kian Kani
Graduate Program in Biochemistry
CSULB
---------------------------------------
GIBBS Version 5 AMBER/UCSF(1997)
--------------------------------------
[-O]verwriting output
File Assignments:
-----------------
|PIN : gibbs1.in
|POUT : gibbs1.out
|PCOORD : PCOORD
|PVEL : PVEL
|PEN : PEN
|PPARM : myo1.top
|PINCRD : myo1.crd
|PREFC : PREFC
|PREST : PREST
|PINFO : PINFO
|MICSTAT : MICSTAT
|CONSTMAT: CONSTMAT
|CNSTSCRT: CNSTSCRT
|PATNRG : PATNRG
Here is the input file:
Input file for equilibration at 0 using gibbs
&cntrl
nrun=1, ntsd=100, tol=1e-05,
idifrg=1, init=3, almdel=0.01,
ntpr=100, irest=0, nsnb=50,
nstmeq=10001, cut=6.0, ntf=3,
npscal=0, ntb=2, dt=0.001,
ntc=3, ntwx=1000, nstmul=1500,
temp0=300, dielc=1.0, ielper=-1,
ncorc=1, isldyn=3, tempi=300,
ntp=1, almda=1, nstlim=10000,
intprt=5, idiel=1, ntx=1,
scee=1.2,
&end
-------------------------------------------------------------------------------
READING MOLECULAR TOPOLOGY FILE (PPARM)
--------------------
DYNAMIC MEMORY
ALLOCATED USED
| INTEGER: 3750000 156197
| REAL: 1500000 168367
| CHARACTER: 125000 15336
| AVAILABLE INTEGER WORDS x 1 N-B PAIRS/WORD = 3593803 MAXIMUM N-B PAIRS
--------------------
Title line from parm:
CONTROL FLAGS FOR THIS RUN
--------------------------
Input file for equilibration at 0 using gibbs
THE TIME LIMIT FOR THE JOB = 1000000.
THE RESTART PARAMETER = 0 (irest )
THE FLAG FOR BELLY OPTION = 0 (ibelly)
THE FLAG FOR DNA CHARGE CHANGE = 0 (ichdna)
THE FLAG FOR POLARIZATION = 0 (ipol )
THE FLAG FOR 3bods = 0 (i3bod )
# of atoms = 2499
NSM = 0 NRAM = 0 NTX = 1
NTXO = 1 ISEED = 71277
TempI = 300.000 HEAT = 0.000
NTB = 2 IFTRES= 1 BOXX = 0.000
BOXY = 0.000 BOXZ = 0.000 BETA = 0.000
NRUN = 1 NTT = 1 TEMP0 = 300.000
DTEMP = 10.000 TAUTP = 0.200 TAUTS = 0.200
ISOLVP= 0 NSEL = 0 DTUSE = 1.000
NTP = 1 NPSCAL= 0 PRES0 = 1.000
COMP = 44.600 TAUP = 0.200
NTCM = 0 NSCM = 90000000
ISVAT = 1
NSTLIM= 10000 INIT = 3
T = 0.00000 DT = 0.00100
VLIMIT= 0.000 IVEMAX= 0
NTC = 3
TOL = 0.00001 TOLR2 = 0.00010
NCORC = 1 ISHKFL= 1 ITIMTH= 0
JFASTW= 0
NTF = 3 NTID = 0
NTNB = 1 NSNB = 50 IDIEL = 1
IELPER= -1 IMGSLT= 0 IDSX0 = 0
ITRSLU= 1
IOLEPS= 0 INTPRT= 5 ITIP = 0
CUT = 6.00000 SCNB = 2.00000
SCEE = 1.20000 DIELC = 1.00000
CUT2ND= 0.00000 CUTPRT= 0.00000
NTPR = 100 NTWX = 1000 NTWV = -1
NTWE = -1 NTWXM = 999999 NTWVM = 999999
NTWEM = 999999 IOUTFM= 0
ISANDE= 0 IPERAT= 0 IATCMP= 0
NTATDP= 0 ICMPDR= 0 NCMPDR= 0
NTWPRT= 0 NTWPR0= 0
NTR = 0 NRC = 0 NTRX = 1
TAUR = 1.000 INTR = 0 IBIGM = 1
IDUM1 = 0 NMRMAX= 0 IWTMAX = 0
ISFTRP= 0 RWELL = 5.00000
IFTIME= 1 CTIMT = 0.00000
ALMDA = 1.0000000 ALMDEL = 0.0100000
ISLDYN= 3 IDIFRG= 1
NSTMEQ= 10001 NSTMUL= 1500 NDMPMC= 0
IDWIDE= 0 IBNDLM= 0
IFTIME= 0 CTIMT =
NSTPE = 2 NSTPA = 2
DTE = 0.00100 DTA = 0.00100
IVCAP = 0 MATCAP= 0 IFCAP = 0
NATCAP= 0 CUTCAP= 0.00000
XCAP = 0.00000 YCAP = 0.00000
ZCAP = 0.00000 FCAP = 1.50000
Water definition for fast 3pt model:
Resname = WAT ; Oxygen_name = O ; Hyd_name1 = H1 ; Hyd_name2 = H2
CUT must be < half smallest box dimension
Box requested (NTB.ne.0) but no setup in parm
Received on Tue Jun 05 2001 - 09:42:48 PDT
