Dear Dr. Thomas Steinbrecher
thanks for your reply.
I changed input file:
min_v0
&cntrl
imin = 1, ntx = 1,
maxcyc = 2000,
ntpr = 100,
ntf = 2, ntc = 2,
ntb = 1, cut = 10.0,
icfe = 1, clambda = 0.1,
ifsc = 0,
crgmask =""
scmask =""
/
------------------------------------------------------
min_v1
&cntrl
imin = 1, ntx = 1,
maxcyc = 2000,
ntpr = 100,
ntf = 2, ntc = 2,
ntb = 1, cut = 10.0,
icfe = 1, clambda = 0.1,
ifsc = 0,
crgmask = "DG9.O6,H1,N2,H21,H22 DC18.N4,H41,H42,H5"
scmask =""
/
Is crgmask = "DG9.O6,H1,N2,H21,H22 DC18.N4,H41,H42,H5" true?
Now, when I use mpirun -np 2 $AMBERHOME/bin/sander.MPI -ng 2 -groupfile
min.group & , I encounter with
Running multisander version of sander amber10
Total processors = 2
Number of groups = 2
Error in group input::atommask.f::selectElemMask
elementary mask does not start with : or .
-----------------------------------------------------------------------------
One of the processes started by mpirun has exited with a nonzero exit
code. This typically indicates that the process finished in error.
If your process did not finish in error, be sure to include a "return
0" or "exit(0)" in your C code before exiting the application.
PID 27680 failed on node n0 (217.218.85.50) with exit status 1.
-----------------------------------------------------------------------------
output file is as follows:
| Run on 02/07/2012 at 20:54:31
[-O]verwriting output
File Assignments:
| MDIN: free_1_min_v0_0.1.in
| MDOUT: free_tg_1_min_v0_0.1.out
|INPCRD: free_tg_1_v0_0.1.inpcrd
| PARM: free_tg_1_v0_0.1.prmtop
|RESTRT: free_tg_1_min_v0_0.1.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: free_tg_1_min_v0_0.1.mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip
|INPTRA: inptraj
|
Here is the input file:
free_1_min_v0_0.1
&cntrl
imin = 1, ntx = 1,
maxcyc = 2000,
ntpr = 100,
ntf = 2, ntc = 2,
ntb = 1, cut = 10.0,
icfe = 1, clambda = 0.1,
ifsc = 0,
crgmask =""
scmask =""
/
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags: MPI
getting new box info from bottom of inpcrd
| INFO: Old style inpcrd file read
| peek_ewald_inpcrd: Box info found
|Largest sphere to fit in unit cell has radius = 33.230
| New format PARM file being parsed.
| Version = 1.000 Date = 02/01/12 Time = 16:21:23
NATOM = 23049 NTYPES = 18 NBONH = 22498 MBONA = 590
NTHETH = 704 MTHETA = 907 NPHIH = 1492 MPHIA = 1606
NHPARM = 0 NPARM = 0 NNB = 34209 NRES = 7450
NBONA = 590 NTHETA = 907 NPHIA = 1606 NUMBND = 39
NUMANG = 76 NPTRA = 42 NATYP = 28 NPHB = 1
IFBOX = 1 NMXRS = 34 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 1536370
| Hollerith 145746
| Integer 580836
| Max Pairs 13276224
| nblistReal 276588
| nblist Int 941643
| Total 72540 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
BOX TYPE: RECTILINEAR
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
General flags:
imin = 1, nmropt = 0
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 100, ntrx = 1, ntwr =
500
iwrap = 0, ntwx = 0, ntwv = 0, ntwe
= 0
ioutfm = 0, ntwprt = 0, idecomp = 0,
rbornstat= 0
Potential function:
ntf = 2, ntb = 1, igb = 0, nsnb
= 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 10.00000, intdiel = 1.00000
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Energy minimization:
maxcyc = 2000, ncyc = 10, ntmin = 1
dx0 = 0.01000, drms = 0.00010
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00001
Free energy options:
icfe = 1, ifsc = 0
klambda = 1
clambda = 0.10000
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme
= 1
vdwmeth = 1, eedmeth = 1, netfrc = 0
Box X = 66.461 Box Y = 67.010 Box Z = 67.045
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 72 NFFT2 = 72 NFFT3 = 72
Cutoff= 10.000 Tol =0.100E-04
Ewald Coefficient = 0.27511
Interpolation order = 4
| MPI Timing options:
| profile_mpi = 0
what is reason of stopping?
I'm beginner in amber. please guide me.
best regards.
On Tue, Feb 7, 2012 at 12:34 PM, <steinbrt.rci.rutgers.edu> wrote:
> Hi,
>
> > forrtl: severe (24): end-of-file during read, unit 5, file
> > /home/free_1_0.1/
> > min_v1.in, line 13, position 0
>
> sander does not recognize something in your mdin file or expects something
> else before it ends.
>
> > Here is the input file:
> >
> > free_1_min_v0_0.1
> > &cntrl
> > imin = 1, ntx = 1,
> > maxcyc = 2000,
> > ntpr = 100,
> > ntf = 2, ntc = 2,
> > ntb = 1, cut = 10.0,
> > icfe = 1, clambda = 0.1
> > ifsc = 0,
> > crgmask ="
> > scmask ="
> > /
>
> you need closing quotes after each ". An empty string looks like this: ""
> or this '' (two double quotes or two single quotes). Also, it's a guess,
> but try adding commas, after every command...
>
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Feb 07 2012 - 02:00:02 PST
