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
Received on Tue Oct 29 2002 - 00:24:58 PST
