Oh yeah. Thanks so much Mr. Simmerling. It's working when I run from /home
account. I did not notice that.
Thank you very much for your help.
chinsu
On Thu, Mar 11, 2010 at 7:37 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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
> > > > _______________________________________________
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> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
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> > >
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> >
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Received on Thu Mar 11 2010 - 04:00:06 PST
