AMBER Archive (2008)

Subject: Re: AMBER: Simple Minimization - Error

From: Daniel Smith (das92_at_pitt.edu)
Date: Thu Apr 03 2008 - 15:10:28 CDT

Sander is trying to open the file 'refc' for the reference coordinates
for your Cartesian restraints. Your sander line should look like:

sander -O .... -ref hgh_sol_apr3.inpcrd

or whatever your input coordinates are.

Daniel Smith

Graduate Student
Mathematics
University of Pittsburgh

dpandit_at_brandeis.edu wrote:
> Hi:
> I am trying to perform simple minimization but my .out file shows error
>
> Unit 10 Error on OPEN: refc.
>
> I have posted the file message below. I do not understand the error I
> receive. Please help!
>
> THX
> Deepa
>
> -------------------------------------------------------
> Amber 9 SANDER 2006
> -------------------------------------------------------
>
> | Run on 04/03/2008 at 15:44:44
> [-O]verwriting output
>
> File Assignments:
> | MDIN: min_sol1_amb_apr2.in
> | MDOUT: min_sol1_amb_apr2.out
> |INPCRD: hgh_sol_apr3.inpcrd
> | PARM: hgh_sol_apr3.prmtop
> |RESTRT: hgh_sol_apr3.rst
> | REFC: refc
> | MDVEL: mdvel
> | MDEN: mden
> | MDCRD: mdcrd
> |MDINFO: mdinfo
> |INPDIP: inpdip
> |RSTDIP: rstdip
>
>
> Here is the input file:
>
> Stage 1 - Initial Solvent minimization - Protein Fixed
> &cntrl
> imin=1, maxcyc=200,
> ntpr=5,
> ntr=1,
> restraint_wt = 100.0,
> restraintmask=' :1 - 190',
> /
>
>
> --------------------------------------------------------------------------------
>
> 1. RESOURCE USE:
> --------------------------------------------------------------------------------
>
>
> | Flags: MPI
> 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 = 31.250
> | New format PARM file being parsed.
> | Version = 1.000 Date = 04/03/08 Time = 15:29:11
> NATOM = 29828 NTYPES = 17 NBONH = 28293 MBONA = 1563
> NTHETH = 3411 MTHETA = 2111 NPHIH = 6556 MPHIA = 5260
> NHPARM = 0 NPARM = 0 NNB = 52449 NRES = 9125
> NBONA = 1563 NTHETA = 2111 NPHIA = 5260 NUMBND = 43
> NUMANG = 88 NPTRA = 42 NATYP = 30 NPHB = 1
> IFBOX = 2 NMXRS = 24 IFCAP = 0 NEXTRA = 0
> NCOPY = 0
>
>
> | Memory Use Allocated
> | Real 2083964
> | Hollerith 188095
> | Integer 893205
> | Max Pairs 9942666
> | nblistReal 357936
> | nblist Int 1242211
> | Total 66992 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 = 5, 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 = 8.00000, intdiel = 1.00000
> scnb = 2.00000, scee = 1.20000
>
> Frozen or restrained atoms:
> ibelly = 0, ntr = 1
>
> Energy minimization:
> maxcyc = 200, ncyc = 10, 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 = 76.548 Box Y = 76.548 Box Z = 76.548
> Alpha = 109.471 Beta = 109.471 Gamma = 109.471
> NFFT1 = 80 NFFT2 = 80 NFFT3 = 80
> Cutoff= 8.000 Tol =0.100E-04
> Ewald Coefficient = 0.34864
> Interpolation order = 4
>
> Unit 10 Error on OPEN: refc
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu