AMBER Archive (2003)

Subject: NOESY restraints

From: Teletchéa Stéphane (steletch_at_biomedicale.univ-paris5.fr)
Date: Fri Jun 20 2003 - 06:28:03 CDT


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_at_biomedicale.univ-paris5.fr
*~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~*
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