Dear Professor Case
The input files are:
run: MD
&cntrl
imin = 0, irest = 0 , ntx = 1,
nstlim = 2500000, dt = 0.002,
ntc = 2 , ntf = 2,
ntt = 3, gamma_ln = 2.0,
tempi = 298.0, temp0 =298.0,
ntb = 1 ,
ntpr = 250 , ntwx = 250, ntwr = 500 ,
cut = 9,
ig = -1
ioutfm = 1
nmropt=1,
ntr=1
/
&ewald
nfft1 = 90,
nfft2 = 90,
nfft3 = 90,
/
&wt type='DUMPFREQ', istep1=1, /
&wt type='END' /
DISANG=dist_chi.RST
DUMPAVE=restraint.log
LISTIN=POUT
LISTOUT=POUT
Keep DNA fixed with weak restraints
0.05
RES 1 48
END
END
dist_chi.RST:
&rst iat=-1,-1,
ninc=0,ir6=0,ifntyp=0,nstep1=1,nstep2=100000,
r1=0.0000E+00,r2=18.0000,r3=18.0000,r4=100.000,rk2=5,rk3=5,
igr1 =
157,158,159,160,161,164,166,167,169,170,172,173,174,175,178,179,
181,182,183,185,188,189,190,191,192,193,196,198,199,201,202,204,205,209,210,211,
213,214,215,217,220,536,537,538,539,540,543,545,546,548,549,551,552,553,554,557,
558,560,561,562,564,567,568,569,570,571,572,575,577,578,580,581,583,584,588,589,
590,594,596,599,
igr2 =
915,916,917,918,919,922,924,925,927,928,930,931,932,933,936,937,
940,941,943,946,947,948,949,950,951,954,956,957,959,960,962,963,967,968,969,971,
972,973,975,978,1294,1295,1296,1297,1298,1301,1303,1304,1306,1307,1309,1310,1311
,1312,1315,1316,1319,1320,1322,1325,1326,1327,1328,1329,1330,1333,1335,1336,1338
,1339,1341,1342,1346,1347,1348,1350,1351,1352,1354,1357/
and the error is:
-------------------------------------------------------
Amber 10 SANDER 2008
-------------------------------------------------------
| PMEMD implementation of SANDER, Release 10
| Run on 04/11/2012 at 16:32:56
[-O]verwriting output
File Assignments:
| MDIN: run_md.in
| MDOUT: dimero_water_SCP_md.out
| INPCRD: dimero_water_SPC.inpcrd
| PARM: dimero_water_SPC.prmtop
| RESTRT: dimero_water_SPC_md.rst
| REFC: dimero_water_SPC.inpcrd
| MDVEL: mdvel
| MDEN: dimero_water_SPC_md.en
| MDCRD: dimero_water_SPC_md.mdcrd
| MDINFO: mdinfo
|LOGFILE: logfile
Here is the input file:
run: MD
&cntrl
imin = 0, irest = 0 , ntx = 1,
nstlim = 2500000, dt = 0.002,
ntc = 2 , ntf = 2,
ntt = 3, gamma_ln = 2.0,
tempi = 298.0, temp0 =298.0,
ntb = 1 ,
ntpr = 250 , ntwx = 250, ntwr = 500 ,
cut = 9,
ig = -1
ioutfm = 1
nmropt=1,
ntr=1
/
&ewald
nfft1 = 90,
nfft2 = 90,
nfft3 = 90,
/
&wt type='DUMPFREQ', istep1=1, /
&wt type='END' /
DISANG=dist_chi.RST
DUMPAVE=restraint.log
LISTIN=POUT
LISTOUT=POUT
Keep DNA fixed with weak restraints
0.05
RES 1 48
END
END
| Conditional Compilation Defines Used:
| DIRFRC_EFS
| DIRFRC_NOVEC
| MPI
| SLOW_NONBLOCKING_MPI
| PUBFFT
| FFTLOADBAL_2PROC
| Largest sphere to fit in unit cell has radius = 35.598
| New format PARM file being parsed.
| Version = 1.000 Date = 09/30/11 Time = 16:42:41
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
getting new box info from bottom of inpcrd
NATOM = 43314 NTYPES = 19 NBONH = 42238 MBONA = 1088
NTHETH = 1280 MTHETA = 1672 NPHIH = 2588 MPHIA = 3040
NHPARM = 0 NPARM = 0 NNB = 64116 NRES = 14050
NBONA = 1088 NTHETA = 1672 NPHIA = 3040 NUMBND = 43
NUMANG = 86 NPTRA = 48 NATYP = 30 NPHB = 1
IFBOX = 2 NMXRS = 34 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Coordinate Index Table dimensions: 14 14 14
| Direct force subcell size = 6.2283 6.2283 6.2283
BOX TYPE: TRUNCATED OCTAHEDRON
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
General flags:
imin = 0, nmropt = 1
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 250, ntrx = 1, ntwr =
500
iwrap = 0, ntwx = 250, ntwv = 0, ntwe =
0
ioutfm = 1, 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 = 9.00000, intdiel = 1.00000
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 1
Molecular dynamics:
nstlim = 2500000, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00200, vlimit = 20.00000
Langevin dynamics temperature regulation:
ig = -1
temp0 = 298.00000, tempi = 298.00000, gamma_ln= 2.00000
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00001
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 = 250
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme =
1
vdwmeth = 1, eedmeth = 1, netfrc = 1
Box X = 87.197 Box Y = 87.197 Box Z = 87.197
Alpha = 109.471 Beta = 109.471 Gamma = 109.471
NFFT1 = 90 NFFT2 = 90 NFFT3 = 90
Cutoff= 9.000 Tol =0.100E-04
Ewald Coefficient = 0.30768
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=dist_chi.RST
rfree: Error decoding variable 1 3 from:
DUMPAVE=restraint.log
2012/4/11 David A Case <case.biomaps.rutgers.edu>
> On Wed, Apr 11, 2012, Elisa Frezza wrote:
> >
> > Thank you for your answer.
> > Before to write this input file, I used separately nmropt=1 and ntr=1,
> and
> > there was not problems and the group were read in the correct way.
> > This is my input:
> >
> > run: MD
> > &cntrl
> > imin = 0, irest = 0 , ntx = 1,
> > nstlim = 2500000, dt = 0.002,
> > ntc = 2 , ntf = 2,
> > ntt = 3, gamma_ln = 2.0,
> > tempi = 298.0, temp0 =298.0,
> > ntb = 1 ,
> > ntpr = 250 , ntwx = 250, ntwr = 500 ,
> > cut = 9,
> > ig = -1
> > ioutfm = 1
> > nmropt=1,
> > ntr=1
> > /
> > &ewald
> > nfft1 = 90,
> > nfft2 = 90,
> > nfft3 = 90,
> > /
> > &wt type='DUMPFREQ', istep1=1, /
> > &wt type='END' /
> > DISANG=dist_chi.RST
> > DUMPAVE=restraint.log
> > LISTIN=POUT
> > LISTOUT=POUT
> > &end
> ^^^^^^^ It still looks like this line is wrong. What happens if you
> remove
> this line?
>
> When posting, please give the input file and the relevant error in the
> output
> file for that particular input.
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Elisa Frezza
Ph.D. Student in Materials Science and Engineering
Dipartimento di Scienze Chimiche
Università di Padova
via Marzolo, 1
35131 Padova - Italy
Phone: +39 049 827 5149
Skype: elisa.frezza
Emai: elisa.frezza.gmail.com
elisa.frezza.studenti.unipd.it
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Received on Wed Apr 11 2012 - 08:00:06 PDT
