why don't you go to /home/sutr0003/amber-data/ and run Amber from there? Are
you using a batch queue system like PBS? you don't need to be (or want to
be) in the actual Amber directory to run it.
the files input and output are listed in the manual (page 23 for Amber10).
-inf specifies the info file.
On Thu, Mar 11, 2010 at 6:31 AM, Chinh Su Tran To
<chinh.sutranto.gmail.com>wrote:
> Yeah, you are right.
> Im running as a user on the server. I added all the path poiting to my
> account in the batch file, but i dont know how to do it for the mdinfo file
> b/c I could not find its location.
> I dont have the permission to write on the amber folder.
>
> please advice me.
> Thank you.
>
> On Thu, Mar 11, 2010 at 7:27 PM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > 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
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Thu Mar 11 2010 - 04:00:05 PST
