I have been trying to use a system with restrains but do not get any
result I am pasting the mdin file and the mdout file. The mdout file
stops at "5. REFERENCE ATOM COORDINATES" and does not proceed beyond
that 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
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Received on Sun Sep 17 2006 - 06:07:25 PDT
