it's an output file specified on the sander command line. do you have
permission to write in the directory where you are running? I notice that
all of your other outputs have a full path specification, but mdinfo is left
at the default of writing in the current directory. perhaps you forgot to
specify it.
On Thu, Mar 11, 2010 at 5:34 AM, Chinh Su Tran To
<chinh.sutranto.gmail.com>wrote:
> 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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>
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Received on Thu Mar 11 2010 - 03:30:04 PST
