Dear Amber users,
I'm trying to use pmemd or pmemd.MPI with NMR distance restraints.
When I run sander or sander.MPI, the job goes well (see attachment).
However, if I use pmemd or pmemd.MPI (with the same input files) I get this
error:
rfree: Error decoding variable 1 3 from:
DUMPAVE=restrained_atoms_min1.out
Here is my output file:
-------------------------------------------------------
Amber 11 SANDER 2010
-------------------------------------------------------
| PMEMD implementation of SANDER, Release 11
| Run on 04/08/2011 at 18:01:29
[-O]verwriting output
File Assignments:
| MDIN: cpx_mir_iw_min1.in
| MDOUT:
cpx_mir_iw_min1.out
| INPCRD:
cpx_mir_iw.inpcrd
| PARM:
cpx_mir_iw.prmtop
| RESTRT:
cpx_mir_iw_min1.rst
| REFC:
cpx_mir_iw.inpcrd
| MDVEL:
mdvel
| MDEN:
mden
| MDCRD:
mdcrd
| MDINFO:
mdinfo
|LOGFILE:
logfile
Here is the input file:
PME
&cntrl
imin=1, ntx=1,
maxcyc=6000,
ntpr=100,
ntmin=1,
ncyc=500,
ntf=1,
cut=10,
ntb=1,
ntr=1,
nmropt=1,
&end
&wt type='DUMPFREQ', istep1=1
/
&wt type='END'
/
DISANG=restrained_atoms.RST
DUMPAVE=restrained_atoms_min1.out
LISTIN=POUT
LISTOUT=POUT
Hold the protein
100.0
RES 1
1043
END
END
| Conditional Compilation Defines Used:
| DIRFRC_COMTRANS
| DIRFRC_EFS
| DIRFRC_NOVEC
| MPI
| PUBFFT
| FFTLOADBAL_2PROC
| BINTRAJ
| Largest sphere to fit in unit cell has radius = 50.341
| New format PARM file being parsed.
| Version = 1.000 Date = 04/07/11 Time = 18:55:26
| Note: 1-4 EEL scale factors were NOT found in the topology file.
| Using default value of 1.2.
| Note: 1-4 VDW scale factors were NOT found in the topology file.
| Using default value of 2.0.
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
getting new box info from bottom of inpcrd
NATOM = 137593 NTYPES = 22 NBONH = 129370 MBONA = 8438
NTHETH = 18075 MTHETA = 11548 NPHIH = 34241 MPHIA = 29098
NHPARM = 0 NPARM = 0 NNB = 251036 NRES = 41508
NBONA = 8438 NTHETA = 11548 NPHIA = 29098 NUMBND = 84
NUMANG = 187 NPTRA = 100 NATYP = 47 NPHB = 1
IFBOX = 1 NMXRS = 34 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Coordinate Index Table dimensions: 19 16 23
| Direct force subcell size = 6.0476 6.2926 6.0925
BOX TYPE: RECTILINEAR
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
General flags:
imin = 1, nmropt = 1
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 100, ntrx = 1, ntwr =
600
iwrap = 0, ntwx = 0, ntwv = 0, ntwe
= 0
ioutfm = 0, ntwprt = 0, idecomp = 0,
rbornstat= 0
Potential function:
ntf = 1, ntb = 1, igb = 0, nsnb =
25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 10.00000, intdiel = 1.00000
Frozen or restrained atoms:
ibelly = 0, ntr = 1
Energy minimization:
maxcyc = 6000, ncyc = 500, ntmin = 1
dx0 = 0.01000, drms = 0.00010
NMR refinement options:
iscale = 0, noeskp = 1, ipnlty = 1, mxsub
= 1
scalm = 100.00000, pencut = 0.10000, tausw = 0.10000
| Intermolecular bonds treatment:
| no_intermolecular_bonds = 1
| Energy averages sample interval:
| ene_avg_sampling = 1
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme
= 1
vdwmeth = 1, eedmeth = 1, netfrc = 0
Box X = 114.904 Box Y = 100.682 Box Z = 140.127
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 120 NFFT2 = 108 NFFT3 = 144
Cutoff= 10.000 Tol =0.100E-04
Ewald Coefficient = 0.27511
Interpolation order = 4
| PMEMD ewald parallel performance parameters:
| block_fft = 0
| fft_blk_y_divisor = 2
| excl_recip = 0
| excl_master = 0
| atm_redist_freq = 320
LOADING THE CONSTRAINED ATOMS AS GROUPS
5. REFERENCE ATOM COORDINATES
----- READING GROUP 1; TITLE:
DISANG=restrained_atoms.RST
rfree: Error decoding variable 1 3 from:
DUMPAVE=restrained_atoms_min1.out
Could anybody help me to deal with this problem?
Thank you very much in advance.
Miriam
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Received on Fri Apr 08 2011 - 11:30:05 PDT
