Re: [AMBER] mdinfor error

From: Chinh Su Tran To <chinh.sutranto.gmail.com>
Date: Thu, 11 Mar 2010 19:31:23 +0800

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...
> >
> >