I am running Amber 9, starting with minimization, but got the " *Unit 7
Error on OPEN: mdinfo*". Could you please help me what the mdinfo file here?
I checked in the input file, but could not find out what the mdinfo means.
Thank you.
And this is my result:
-------------------------------------------------------
Amber 9 SANDER 2006
-------------------------------------------------------
| Run on 03/11/2010 at 18:17:55
[-O]verwriting output
File Assignments:
| MDIN: /home/sutr0003/amber-data/hla-wat-min1.in
| MDOUT:
/home/sutr0003/amber-data/com-wat.min1.out
|INPCRD:
/home/sutr0003/amber-data/com-wat.crd
| PARM:
/home/sutr0003/amber-data/com-wat.top
|RESTRT:
/home/sutr0003/amber-data/com-wat.min1.rst
| REFC:
/home/sutr0003/amber-data/com-wat.crd
| MDVEL:
mdvel
| MDEN:
mden
| MDCRD:
mdcrd
|MDINFO:
mdinfo
|INPDIP:
inpdip
|RSTDIP:
rstdip
|INPTRA:
inptraj
|
Here is the input file:
#HLA-wat running initial minimization by
sander
&cntrl
imin=1,
maxcyc=1000,
ncyc=500,
ntb=1,
ntr=1,
cut=10.0,
ntpr=10,
/
hold the model
fixed
500.0
RES 50
180
END
END
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
|
Flags:
getting new box info from bottom of inpcrd
| INFO: Old style inpcrd file read
| peek_ewald_inpcrd: Box info found
|Largest sphere to fit in unit cell has radius = 38.795
| New format PARM file being parsed.
| Version = 1.000 Date = 03/11/10 Time = 18:06:28
NATOM = 58792 NTYPES = 17 NBONH = 56806 MBONA = 2013
NTHETH = 4714 MTHETA = 2711 NPHIH = 8759 MPHIA = 6869
NHPARM = 0 NPARM = 0 NNB = 95394 NRES = 18504
NBONA = 2013 NTHETA = 2711 NPHIA = 6869 NUMBND = 34
NUMANG = 68 NPTRA = 36 NATYP = 26 NPHB = 1
IFBOX = 2 NMXRS = 24 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 3847229
| Hollerith 371258
| Integer 1595704
| Max Pairs 33864192
| nblistReal 705504
| nblist Int 1975170
| Total 183249 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
BOX TYPE: TRUNCATED OCTAHEDRON
--------------------------------------------------------------------------------
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 = 10, 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 = 1, igb = 0, nsnb =
25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 10.00000, intdiel = 1.00000
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 1
Energy minimization:
maxcyc = 1000, ncyc = 500, ntmin = 1
dx0 = 0.01000, drms = 0.00010
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme
= 1
vdwmeth = 1, eedmeth = 1, netfrc = 0
Box X = 95.028 Box Y = 95.028 Box Z = 95.028
Alpha = 109.471 Beta = 109.471 Gamma = 109.471
NFFT1 = 96 NFFT2 = 96 NFFT3 = 96
Cutoff= 10.000 Tol =0.100E-04
Ewald Coefficient = 0.27511
Interpolation order = 4
LOADING THE CONSTRAINED ATOMS AS GROUPS
5. REFERENCE ATOM COORDINATES
----- READING GROUP 1; TITLE:
hold the model fixed
GROUP 1 HAS HARMONIC CONSTRAINTS 500.00000
GRP 1 RES 50 TO 180
Number of atoms in this group = 2080
----- END OF GROUP READ -----
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 18247
Sum of charges from parm topology file = -0.00000014
Forcing neutrality...
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
Unit 7 Error on OPEN:
mdinfo
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Received on Thu Mar 11 2010 - 03:00:02 PST
