I'm using amber6.0 with the nmropt=2 option for NMR
refinement of structure from NOESY volumes. I took the
SA NMR refinement exemple script presented p186-187 of
the Manual changing nmropt to 2 and DISANG to NOESY :
&cntrl
nstlim=15000, ntt=1,
scee=1.2,
ntpr=500, pencut=0.1,
ipnlty=1, nmropt=2,
vlimit=10,
ntb=0,
igb=3, mxsub=10, tausw=0.0,
&end
&wt type='TEMP0', istep1=0,istep2=1000,value1=10.,
value2=1200., &end
&wt type='TEMP0', istep1=1001, istep2=3000,
value1=1200.,
value2=1200.0, &end
&wt type='TEMP0', istep1=3001, istep2=15000,
value1=0.,
value2=0.0, &end
&wt type='TAUTP', istep1=0,istep2=3000,value1=0.2,
value2=0.2, &end
&wt type='TAUTP',
istep1=3001,istep2=11000,value1=4.0,
value2=2.0, &end
&wt type='TAUTP',
istep1=11001,istep2=13000,value1=1.0,
value2=1.0, &end
&wt type='TAUTP',
istep1=13001,istep2=14000,value1=0.5,
value2=0.5, &end
&wt type='TAUTP',
istep1=14001,istep2=15000,value1=0.05,
value2=0.05, &end
&wt type='REST', istep1=0,istep2=3000,value1=0.1,
value2=1.0, &end
&wt type='REST', istep1=3001,istep2=15000,value1=1.0,
value2=1.0, &end
&wt type='END', &end
LISTOUT=POUT
NOESY=VOL_RST.dat
My VOL_RST.dat file has been built using makeVOL_RST
program, leading to :
&noeexp
NPEAK = 5* 90, -1,
EMIX = 0.05000, 0.08000, 0.12000, 0.16000,
0.20000,
IHP(1, 1) = 5*277,
JHP(1, 1) = 5*297,
AEXP(1, 1) = 5.76E+05, 7.27E+06, 1.17E+08,
1.17E+07, 3.86E+06,
IHP(1, 2) = 5*284,
JHP(1, 2) = 5*300,
AEXP(1, 2) = 7.36E+06, 9.90E+06, 5.33E+06,
1.06E+07, 2.58E+06,
IHP(1, 3) = 5*294,
JHP(1, 3) = 5*297,
AEXP(1, 3) = 6.08E+06, 9.87E+06, 1.36E+07,
4.28E+07, 2.45E+07,
....
&end
SUBM 1
RES 9 15
END
END
....
&noeexp NPEAK=-1, &end
when I'm launching the run script :
echo 'Annealing processing...'
sander -O \
-i SA_NMRref.dat \
-p $1.top \
-c $1.rst \
-ref $1.rst \
-o ./$1'SA_NMR_l' \
-x ./$1'SA_NMR_c' \
-r ./$1'SA_NMR_rst'
error message appear in *_l file :
....
RESTRAINTS:
Requested file redirections:
LISTOUT = POUT
NOESY = VOL_RST.dat
** No restraint defined **
Done reading weight changes/NMR
restraints
Noesy volumes will be read from file: VOL_RST.dat
Here are comments from the NOEsy input file:
Namelist reports error in reading noeexp
-- Subscript out of range implies dimensioning
problem
-- (see nmr.h and sizes.h, SIZE_NMR_PCY if nmr stuff)
I've compiled amber several times nmr.h and sizes.h
increasing parameters, but error is still there...
#ifdef SIZE_NMR
c
c --- for NMR properties:
c
parameter (MRING=100)
parameter (MSHF=2000)
parameter (MXVAR=300)
parameter (MATOM=3000)
parameter (MA=1000)
parameter (MA2=MA*MA)
parameter (LST=(MA2+MA)/2)
parameter (MXR=1000)
parameter (MXTAU=30)
parameter (MXP=3000)
parameter (MTOT=500000)
parameter (MAXDIP=5000)
parameter (MAXDIPSETS=1000)
#else
for nmr.h and
parameter (MAXREA=2500000)
parameter (MAXINT=2000000)
parameter (MAXHOL=600000)
parameter (MAXPR=20000000)
parameter (MAXDUP=8000)
integer
MAX_RSTACK,MAX_ISTACK,MAX_STACK_PTRS,MAX_HEAP_PTRS
parameter (MAX_RSTACK=16000000)
parameter (MAX_ISTACK=1000000)
parameter (MAX_STACK_PTRS=10000)
parameter (MAX_HEAP_PTRS=10000)
for sizes.h
thank you for help.
Olivier Delalande, PhD student, Paris
--
*~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~*
Teletchéa Stéphane - CNRS UMR 8601
Lab. de chimie et biochimie pharmacologiques et toxicologiques
45 rue des Saints-Pères 75270 Paris cedex 06
tél : (33) - 1 42 86 20 86 - fax : (33) - 1 42 86 83 87
mél : steletch.biomedicale.univ-paris5.fr
*~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~*
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Received on Fri Jun 20 2003 - 12:53:02 PDT
