AMBER Archive (2006)

Subject: AMBER: have problems with restrained minimization

From: Abhilash (mohan.25_at_osu.edu)
Date: Fri Sep 15 2006 - 13:10:50 CDT

I for some reason cannot perform a restrained minimisation with the mdin
file and the output I get are pasted below any pointers will be greatly
appreciated

The mdin file:
--------------
Initial
minimisation
 &cntrl

  imin=1, maxcyc=5000,
ncyc=2000,
  
igb=1,ntb=0,ntr=1,cut=16

 /

restraints

500.0

RES 1
36
END

END
-----------------------------------
The output does not produce any results but stops at this point.

         -------------------------------------------------------
          Amber 8 SANDER Scripps/UCSF 2004
          -------------------------------------------------------

| Run on 09/15/2006 at 14:10:45
  [-O]verwriting output

File Assignments:
| MDIN:
complex_firstmin.mdin
| MDOUT:
complex_firstmin_test.mdout
|INPCRD:
complex.crd
| PARM:
complex.top
|RESTRT:
complex_firstmin_test.rst
| REFC:
complex.top
| MDVEL:
mdvel
| MDEN:
mden
| MDCRD:
mdcrd
|MDINFO:
complex_firstmin_test.mdinfo
|INPDIP:
inpdip
|RSTDIP:
rstdip

 
 Here is the input file:
 
Initial
minimisation
 &cntrl

  imin=1, maxcyc=5000,
ncyc=2000,
  
igb=1,ntb=0,ntr=1,cut=16

 /

restraints

500.0

RES 1
36
END

END

                                                                               

                                                                               

                                                                               

--------------------------------------------------------------------------------
   1. RESOURCE USE:
--------------------------------------------------------------------------------

| Flags:
MPI
| New format PARM file being parsed.
| Version = 1.000 Date = 09/13/06 Time = 21:35:45
 NATOM = 1575 NTYPES = 14 NBONH = 816 MBONA = 764
 NTHETH = 1853 MTHETA = 1031 NPHIH = 3403 MPHIA = 1949
 NHPARM = 0 NPARM = 0 NNB = 8722 NRES = 100
 NBONA = 764 NTHETA = 1031 NPHIA = 1949 NUMBND = 33
 NUMANG = 67 NPTRA = 33 NATYP = 24 NPHB = 0
 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0
 NCOPY = 0

| Memory Use Allocated
| Real 69496
| Hollerith 9552
| Integer 99785
| Max Pairs 1
| Max Rstack 1
| Max Istack 1
| Total 970 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals

--------------------------------------------------------------------------------
   2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------

                                                                                

General flags:
     imin = 1, nmropt = 0

Nature and format of input:
     ntx = 1, irest = 0, ntrx = 1

Nature and format of output:
     ntxo = 1, ntpr = 50, ntrx = 1, ntwr
= 500
     iwrap = 0, ntwx = 0, ntwv = 0, ntwe
= 0
     ioutfm = 0, ntwprt = 0, idecomp = 0,
rbornstat= 0

Potential function:
     ntf = 1, ntb = 0, igb = 1, nsnb
= 25
     ipol = 0, gbsa = 0, iesp = 0
     dielc = 1.00000, cut = 16.00000, intdiel = 1.00000
     saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000
     gbbeta = 0.00000, gbgamma = 0.00000, surften = 0.00500
     rdt = 0.00000, rgbmax = 25.00000
     scnb = 2.00000, scee = 1.20000

Frozen or restrained atoms:
     ibelly = 0, ntr = 1

Energy minimization:
     maxcyc = 5000, ncyc = 2000, ntmin = 1
     dx0 = 0.01000, drms = 0.00010

    LOADING THE CONSTRAINED ATOMS AS GROUPS

   5. REFERENCE ATOM COORDINATES

thanks,
Abhilash Mohan
graduate student,
the ohio state university
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