AMBER Archive (2006)

Subject: Re: AMBER: Long line of input

From: Myunggi Yi (myunggi_at_gmail.com)
Date: Wed Jul 19 2006 - 21:03:11 CDT

The program just can't read the namelist input.
The following is the output.
The atoms have been selected manually.

          -------------------------------------------------------
          Amber 8 SANDER Scripps/UCSF 2004
          -------------------------------------------------------

| Run on 07/19/2006 at 16:40:01
  [-O]verwriting output

File Assignments:
| MDIN: fix2.in
| MDOUT: fix2.out
|INPCRD: cen-eq.rst7
| PARM: m2m-eq.top
|RESTRT: fix2.rst
| REFC: ali-cen-eq.rst7
| MDVEL: mdvel
| MDEN: mden
| MDCRD: fix2.trj
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip

 Here is the input file:

npt fix2
 &cntrl
  nstlim = 50000, dt=.002,
  irest=1, ntpr=500, ntwx=500, ntx=5,
  temp0=310.0, ntt=1,
  tautp=0.4, taup=0.6, cut=9.0,
  ntb=2, ntp=2, iwrap=1,
  ntc=2, ntf=2,
  ntr=1, restraint_wt=5.0,
 restraintmask='(:1-108 & !@H=) | :110,111,114,117,119,120,124,125,128,134,137,
  itgtmd=1,
  tgtrmsmask=':1-108 & !@H=',
 /

--------------------------------------------------------------------------------
  1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags: MPI
 getting new box info from bottom of inpcrd
| peek_ewald_inpcrd: Box info found
|Largest sphere to fit in unit cell has radius = 31.344
| New format PARM file being parsed.
| Version = 1.000 Date = 07/04/06 Time = 21:21:43
 NATOM = 30057 NTYPES = 29 NBONH = 24265 MBONA = 5660
 NTHETH = 20672 MTHETA = 6820 NPHIH = 46647 MPHIA = 13580
 NHPARM = 0 NPARM = 0 NNB = 101164 NRES = 5455
 NBONA = 5660 NTHETA = 6820 NPHIA = 13580 NUMBND = 50
 NUMANG = 100 NPTRA = 55 NATYP = 40 NPHB = 1
 IFBOX = 1 NMXRS = 118 IFCAP = 0 NEXTRA = 0
 NCOPY = 0

| Memory Use Allocated
| Real 2264277
| Hollerith 185799
| Integer 2835310
| Max Pairs 1666911
| Max Rstack 946378
| Max Istack 150285
| Total 43982 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals

     BOX TYPE: RECTILINEAR

--------------------------------------------------------------------------------
  2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------

General flags:
     imin = 0, nmropt = 0

Nature and format of input:
     ntx = 5, irest = 1, ntrx = 1

Nature and format of output:
     ntxo = 1, ntpr = 500, ntrx = 1, ntwr = 500
     iwrap = 1, ntwx = 500, ntwv = 0, ntwe = 0
     ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0

Potential function:
     ntf = 2, ntb = 2, igb = 0, nsnb = 25
     ipol = 0, gbsa = 0, iesp = 0
     dielc = 1.00000, cut = 9.00000, intdiel = 1.00000
     scnb = 2.00000, scee = 1.20000

Frozen or restrained atoms:
     ibelly = 0, ntr = 1

Molecular dynamics:
     nstlim = 50000, nscm = 1000, nrespa = 1
     t = 0.00000, dt = 0.00200, vlimit = 20.00000

Berendsen (weak-coupling) temperature regulation:
     temp0 = 310.00000, tempi = 0.00000, tautp = 0.40000

Pressure regulation:
     ntp = 2
     pres0 = 1.00000, comp = 44.60000, taup = 0.60000

SHAKE:
     ntc = 2, jfastw = 0
     tol = 0.00001

Targeted molecular dynamics:
     tgtrmsd = 0.00000, tgtmdfrc= 0.00000

Ewald parameters:
     verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
     vdwmeth = 1, eedmeth = 1, netfrc = 1
     Box X = 68.414 Box Y = 62.689 Box Z = 68.393
     Alpha = 90.000 Beta = 90.000 Gamma = 90.000
     NFFT1 = 72 NFFT2 = 64 NFFT3 = 72

| Memory Use Allocated
| Real 2264277
| Hollerith 185799
| Integer 2835310
| Max Pairs 1666911
| Max Rstack 946378
| Max Istack 150285
| Total 43982 kbytes
| Max Rstack 946378
| Max Istack 150285
| Total 43982 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals

     BOX TYPE: RECTILINEAR

--------------------------------------------------------------------------------
  2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------

General flags:
     imin = 0, nmropt = 0

Nature and format of input:
     ntx = 5, irest = 1, ntrx = 1

Nature and format o

On 7/19/06, hornak_at_csb.sunysb.edu <hornak_at_csb.sunysb.edu> wrote:
> Dear Myunggi,
>
> you don't say how the program fails - is there a specific error message?
> Is the list of residues defined by distance or is it just a list of
> residues that you manually selected for restraints?
>
> Cheers,
> -Viktor
>
> > Dear Amber users,
> >
> > I'm trying to apply harmonic restraint.
> > How can I solve the problem of long line input?
> > The following is my input.
> >
> > ============================
> > npt
> > &cntrl
> > nstlim = 50000, dt=.002,
> > irest=1, ntpr=500, ntwx=500, ntx=5,
> > temp0=310.0, ntt=1,
> > tautp=0.4, taup=0.6, cut=9.0,
> > ntb=2, ntp=2, iwrap=1,
> > ntc=2, ntf=2,
> > ntr=1, restraint_wt=5.0,
> > restraintmask='(:1-108 & !@H=) |
> > :110,111,114,117,119,120,124,125,128,134,137,138,140,142,148-152,154,155,176,178,180,182,204,213,215_at_P',
> > itgtmd=1,
> > tgtrmsmask=':1-108 & !@H=',
> > /
> > ============================
> >
> >
> >
> > --
> > Best wishes,
> >
> > MYUNGGI YI
> > ==================================
> > KLB 419
> > Institute of Molecular Biophysics
> > Florida State University
> > Tallahassee, FL 32306
> >
> > Office: (850) 645-1334
> > http://www.scs.fsu.edu/~myunggi
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber_at_scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> >
>
>
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> 

-- 
Best wishes,

MYUNGGI YI
==================================
KLB 419
Institute of Molecular Biophysics
Florida State University
Tallahassee, FL 32306

Office: (850) 645-1334
http://www.scs.fsu.edu/~myunggi
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