I try to make example turorial
"Thermodynamic integration calculations using sander
Running the charging calculation in vacuum"
Amd I have that errors
$AMBERHOME/exe/sander -O -i md.in -o eq2.o -c eq1.x -p prmtop.coul.vac -r eq2.x
forrtl: No such file or directory
forrtl: severe (29): file not found, unit 9, file /home/obliczenia/amber8/obliczenia/kasia/PHE/fort.9
Image PC Routine Line Source
sander 08205804 Unknown Unknown Unknown
Stack trace terminated abnormally.
-------------------------------------------------------
Amber 8 SANDER Scripps/UCSF 2004
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| Run on 05/11/2005 at 11:32:04
[-O]verwriting output
File Assignments:
| MDIN: md.in
| MDOUT: eq2.o
|INPCRD: eq1.x
| PARM: prmtop.coul.vac
|RESTRT: eq2.x
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip
Here is the input file:
neutralize toluene
&cntrl
ntr = 0,
nstlim = 100000, nscm = 2000, ntave = 10000,
ntx = 5, irest = 1, ntb = 0, ntpr = 200,
dt = 0.001, nrespa = 2,
ntt = 1, temp0 = 300., tautp = 2.0,
ntc = 2, ntf = 2, tol = 0.000001,
ntwr = 10000, ntwx = 0,
icfe = 1, clambda = 0.5,
&end
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags: MPI
| NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation
When i change parameters
-------------------------------------------------------
Amber 8 SANDER Scripps/UCSF 2004
-------------------------------------------------------
| Run on 05/11/2005 at 11:21:26
[-O]verwriting output
File Assignments:
| MDIN: md.in
| MDOUT: eq2.o
|INPCRD: eq1.x
| PARM: prmtop.coul.vac
|RESTRT: eq2.x
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip
Here is the input file:
neutralize toluene
&cntrl
ntr = 0,
nstlim = 100000, nscm = 2000, ntave = 10000,
ntx = 5, irest = 1, ntb = 0, ntpr = 200,
dt = 0.001, nrespa = 2,
ntt = 1, temp0 = 300., tautp = 2.0,
ntc = 2, ntf = 2, tol = 0.000001,
ntwr = 10000, ntwx = 0,
icfe = 1, clambda = 0.5,
cut = 8.1,
igb = 1,
&end
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags: MPI
| New format PARM file being parsed.
| Version = 1.000 Date = 04/27/05 Time = 11:01:19
NATOM = 15 NTYPES = 4 NBONH = 8 MBONA = 7
NTHETH = 16 MTHETA = 8 NPHIH = 27 MPHIA = 9
NHPARM = 0 NPARM = 0 NNB = 68 NRES = 1
NBONA = 7 NTHETA = 8 NPHIA = 9 NUMBND = 4
NUMANG = 5 NPTRA = 3 NATYP = 4 NPHB = 0
IFBOX = 0 NMXRS = 15 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 566
| Hollerith 93
| Integer 20674
| Max Pairs 1
| Max Rstack 46
| Max Istack 1
| Total 85 kbytes
Running a free energy calculation with lambda = 0.500
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
PHE
General flags:
imin = 0, nmropt = 0
Nature and format of input:
ntx = 5, irest = 1, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 200, ntrx = 1, ntwr = 10000
iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0
ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function:
ntf = 2, ntb = 0, igb = 1, nsnb = 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 8.10000, intdiel = 1.00000
saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000
gbbeta = 0.00000, gbgamma = 0.00000, surften = 0.00500
rdt = 0.00000, rgbmax = 25.00000
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Molecular dynamics:
nstlim = 100000, nscm = 2000, nrespa = 2
t = 0.00000, dt = 0.00100, vlimit = 20.00000
Berendsen (weak-coupling) temperature regulation:
temp0 = 300.00000, tempi = 0.00000, tautp = 2.00000
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00000
Free energy options:
klambda = 1
clambda = 0.50000
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
Unit 9 Error on OPEN: eq1.x
Where from that file eq1.x gets ?????????????
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Received on Wed May 11 2005 - 12:53:00 PDT
