Hello all!
I'm trying to studi a solvated protein with some restraint to the
backbone, but pmemd gives me some errors with reference coordinates and
atoms group.
Can anyone please tell me what the problem is?
Thanks
Emanuele
I attach here the output:
-------------------------------------------------------
Amber 11 SANDER 2010
-------------------------------------------------------
| PMEMD implementation of SANDER, Release 11
| Run on 02/20/2011 at 20:44:22
[-O]verwriting output
File Assignments:
| MDIN:
/home/chimi/dismab1/emanuele/mGluR7/GLC_CAP/pmemd/protocol/heat2.in
| MDOUT: mGluR7_GLC_CAP_heat2.out
| INPCRD: mGluR7_GLC_CAP_heat1.rst
| PARM: mGluR7_GLC_CAP.top
| RESTRT: mGluR7_GLC_CAP_heat2.rst
| REFC: mGluR7_GLC_CAP_heat1.rst
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mGluR7_GLC_CAP_heat2.mdcrd
| MDINFO: mdinfo
|LOGFILE: logfile
Here is the input file:
#Stage 2 heating 50K to 100K NVT ensamble 20ps restraint 8kcal/mol
&cntrl
imin=0, irest=0, ntp=0, ntb=1, ntpr=500, nstlim=10000, ntt=1,
vlimit=10, cut=8, tautp=0.4, ntx=1, ntf=2, ntc=2,
ntwr=500, ntwx=500, lastist=10000000, lastrst=10000000, dt=0.001,
tempi=50.0, temp0=100.0
ntr=1,
&end
Backbone restraints
8.0
FIND
* * M *
SEARCH
RES 1 476
END
END
&end
| WARNING: The sander lastist option is not needed and is ignored.
| WARNING: The sander lastrst option is not needed and is ignored.
| Conditional Compilation Defines Used:
| DIRFRC_COMTRANS
| DIRFRC_EFS
| DIRFRC_NOVEC
| MPI
| PUBFFT
| FFTLOADBAL_2PROC
| BINTRAJ
| Largest sphere to fit in unit cell has radius = 41.619
| New format PARM file being parsed.
| Version = 1.000 Date = 02/08/11 Time = 15:55:21
| 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 = 81335 NTYPES = 18 NBONH = 77816 MBONA = 3588
NTHETH = 7836 MTHETA = 4859 NPHIH = 15126 MPHIA = 11246
NHPARM = 0 NPARM = 0 NNB = 137545 NRES = 25241
NBONA = 3588 NTHETA = 4859 NPHIA = 11246 NUMBND = 53
NUMANG = 114 NPTRA = 53 NATYP = 40 NPHB = 1
IFBOX = 2 NMXRS = 24 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Coordinate Index Table dimensions: 18 18 18
| Direct force subcell size = 5.6636 5.6636 5.6636
BOX TYPE: TRUNCATED OCTAHEDRON
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
General flags:
imin = 0, nmropt = 0
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 500, ntrx = 1, ntwr
= 500
iwrap = 0, ntwx = 500, 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 = 8.00000, intdiel = 1.00000
Frozen or restrained atoms:
ibelly = 0, ntr = 1
Molecular dynamics:
nstlim = 10000, nscm = 0, nrespa = 1
t = 0.00000, dt = 0.00100, vlimit = 10.00000
Berendsen (weak-coupling) temperature regulation:
temp0 = 100.00000, tempi = 50.00000, tautp = 0.40000
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00001
| Intermolecular bonds treatment:
| no_intermolecular_bonds = 1
| Energy averages sample interval:
| ene_avg_sampling = 500
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme
= 1
vdwmeth = 1, eedmeth = 1, netfrc = 1
Box X = 101.945 Box Y = 101.945 Box Z = 101.945
Alpha = 109.471 Beta = 109.471 Gamma = 109.471
NFFT1 = 108 NFFT2 = 108 NFFT3 = 108
Cutoff= 8.000 Tol =0.100E-04
Ewald Coefficient = 0.34864
Interpolation order = 4
| PMEMD ewald parallel performance parameters:
| block_fft = 0
| fft_blk_y_divisor = 4
| excl_recip = 0
| excl_master = 0
| atm_redist_freq = 320
LOADING THE CONSTRAINED ATOMS AS GROUPS
5. REFERENCE ATOM COORDINATES
----- READING GROUP 1; TITLE:
rfree: End of file on unit 5
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Received on Mon Feb 21 2011 - 01:00:04 PST
