It may be that pmemd is sensitive to the ordering of what comes after the
&cntrl namelist. Try putting the group specification that specifies RES 1
1043 immediately after the last namelist, and put everything else after
that.
The manual may provide more help.
Hope this helps,
Jason
On Fri, Apr 8, 2011 at 11:03 AM, miriam sgobba <miriam.sgobba.gmail.com>wrote:
> 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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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Apr 08 2011 - 12:00:06 PDT
