AMBER Archive (2002)

Subject: LEaP: The parm and coord files disagree on the number of atoms

From: Miguel de Federico (miguel_at_qorws1.uab.es)
Date: Tue Oct 29 2002 - 02:24:58 CST

 I'm trying to run a FEP calculation with gibbs, and I get an error
message telling me that the parm and coord files disagree on the number
of atoms.
 The leap commands employed are here. (The unit c6x was in the library
units2.lib)

source leaprc.ff99
loadoff units2.lib
loadamberparams c6x.par
solvatebox c6x WATBOX216 10.0
saveamberparm c6x 100c6x.top 100c6x.crd

 As I got the top and crd file in the same command, how it's possible
they have different number of atoms?

 The gibbs error message is displayed at the end of message.

 Thak you in advance,

Miguel.

          ---------------------------------------
          GIBBS Version 5 AMBER/UCSF(1997)
          --------------------------------------

  [-O]verwriting output
 File Assignments:
 -----------------

|PIN : 100fep1.in
|POUT : 100c6x.out
|PCOORD : 100c6x.trj
|PVEL : PVEL
|PEN : PEN
|PPARM : ../5leap/100c6x.top
|PINCRD : ../5leap/100c6x.crd
|PREFC : PREFC
|PREST : 100c6x.rst
|PINFO : PINFO
|MICSTAT : 100c6x.mst
|CONSTMAT: CONSTMAT
|CNSTSCRT: CNSTSCRT
|PATNRG : PATNRG

 Here is the input file:

Calculo de Perturbación de Energía Libre (FEP)
Temperatura constante 300k
Presion constante
 &cntrl
  ntx=1, ntb=2,
  ntt=1, temp0=300.0, tautp=0.2,
  ntp=1, taup=0.2, isvat=1,
  nstlim=-1,
  ntc=2, scee=1.2,
  ntpr=100, ntpr=100, ntwprt=-1,
  almdel=0.1, isldyn=-3, nstmeq=5, nstmul=5,
  ndmpmc=100,
 &end
-------------------------------------------------------------------------------

                   READING MOLECULAR TOPOLOGY FILE (PPARM)

| New format PARM file being parsed.
| Version = 1.000 Date = 10/29/02 Time = 10:31:21
                             --------------------
                                DYNAMIC MEMORY
                                  ALLOCATED USED
| INTEGER: 3750000 44562
| REAL: 1500000 117369
| CHARACTER: 125000 11658

| AVAILABLE INTEGER WORDS x 1 N-B PAIRS/WORD = 3705438 MAXIMUM N-B
PAIRS
                             --------------------

 Title line from parm:
 c6x

                          CONTROL FLAGS FOR THIS RUN
                          --------------------------

Calculo de Perturbación de Energía Libre (FEP)

     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 = 1745
     NSM = 0 NRAM = 0 NTX = 1
     NTXO = 1 ISEED = 71277
     TempI = 0.000 HEAT = 0.000

     NTB = 2 IFTRES= 1 BOXX = 31.398
     BOXY = 30.511 BOXZ = 29.587 BETA = 90.000

     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=******* INIT = 3
     T = 0.00000 DT = 0.00100
     VLIMIT= 0.000 IVEMAX= 0

     NTC = 2
     TOL = 0.00050 TOLR2 = 0.00010
     NCORC = 0 ISHKFL= 1 ITIMTH= 0
     JFASTW= 0

     NTF = 1 NTID = 0
     NTNB = 1 NSNB = 50 IDIEL = 1
     IELPER= 0 IMGSLT= 0 IDSX0 = 0
     ITRSLU= 1
     IOLEPS= 0 INTPRT= 0 ITIP = 0

     CUT = 8.00000 SCNB = 2.00000
     SCEE = 1.20000 DIELC = 1.00000
     CUT2ND= 0.00000 CUTPRT= 0.00000

     NTPR = 100 NTWX = -1 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= -1 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 = 0.1000000
     ISLDYN= -3 IDIFRG= 0
     NSTMEQ= 5 NSTMUL= 5 NDMPMC= 100
     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

                              ------------------
                              CALCULATION METHOD

 Fixed-width window Free Energy Perturbation
 Delta_lambda = 0.1000000; Simulation direction 1->0
                              ------------------

                  READING ATOMIC COORDINATES AND VELOCITIES
                  -----------------------------------------

 %GIBBS-F-MISMATCH, The parm and coord files disagree on the number of
atoms