You need to examine the files in question directly (they are both
ascii formatted). In the topology file the first entry in line 2
is the number of atoms, the same for the coordinate file. If they
don't agree, the best thing is to delete both files and rerun
leap (just to make sure that leap is actually making the files you
ask it to). Then reexamine the new files.
jim
On Tue, 29 Oct 2002, Miguel de Federico wrote:
> 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
>
>
--
----------------------------------------------------------------------------
James W. Caldwell (voice) 415-476-8603
Department of Pharmaceutical Chemistry (fax) 415-502-1411
Mail Stop 0446 (email) caldwell_at_heimdal.ucsf.edu
513 Parnassus Avenue
University of California
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Received on Tue Oct 29 2002 - 07:50:26 PST
