Hi,
I am having trouble in minimization. It seems it got stuck at a point, no
error messages but its not moving further. Any suggestions?
I am posting my min.out file here.
-------------------------------------------------------
Amber 10 SANDER 2008
-------------------------------------------------------
| Run on 06/06/2012 at 13:45:07
[-O]verwriting output
File Assignments:
| MDIN: min.in
| MDOUT:
Dock_ste_min.out
|INPCRD:
Dock_ste.inpcrd
| PARM:
Dock_ste.prmtop
|RESTRT:
Dock_ste_min.crd
| REFC:
refc
| MDVEL:
mdvel
| MDEN:
mden
| MDCRD:
mdcrd
|MDINFO:
mdinfo
|INPDIP:
inpdip
|RSTDIP:
rstdip
Here is the input file:
Mini
input
&cntrl
imin=1, maxcyc = 750, ncyc =
750,
ntb = 0, igb = 1, cut =
10,
ntpr =
100
&end
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
|
Flags:
| New format PARM file being parsed.
| Version = 1.000 Date = 06/05/12 Time = 11:02:04
NATOM = 37422 NTYPES = 16 NBONH = 35100 MBONA = 2381
NTHETH = 5166 MTHETA = 3231 NPHIH = 9926 MPHIA = 7919
NHPARM = 0 NPARM = 0 NNB = 69152 NRES = 11229
NBONA = 2381 NTHETA = 3231 NPHIA = 7919 NUMBND = 46
NUMANG = 98 NPTRA = 44 NATYP = 30 NPHB = 1
IFBOX = 1 NMXRS = 82 IFCAP = 0 NEXTRA = 0
NCOPY = 0
Implicit solvent radii are modified Bondi radii
(mbondi)
| Memory Use Allocated
| Real 2395588
| Hollerith 235763
| Integer 828038
| Max Pairs 1
| nblistReal 0
| nblist Int 0
| Total 22871 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
BOX TYPE: RECTILINEAR
--------------------------------------------------------------------------------
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 = 100, 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 = 0, igb = 1, nsnb
= 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 10.00000, intdiel = 1.00000
saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000
gbbeta = 0.00000, gbgamma = 0.00000, surften = 0.00500
rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.50000
alpb = 0
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Energy minimization:
maxcyc = 750, ncyc = 750, ntmin = 1
dx0 = 0.01000, drms = 0.00010
| INFO: Old style inpcrd file read
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 10940
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
NSTEP ENERGY RMS GMAX NAME NUMBER
1 NaN NaN 5.8908E+01 O 23176
BOND = 446645.5044 ANGLE = 1672.6266 DIHED =
3358.8277
VDWAALS = ************* EEL = -73662.8982 EGB =
NaN
1-4 VDW = 999.3677 1-4 EEL = 11112.3672 RESTRAINT =
0.0000
Asma
On Wed, Jun 6, 2012 at 6:40 PM, Jason Swails <jason.swails.gmail.com> wrote:
> try adding a blank line at the bottom of the file.
>
> On Wed, Jun 6, 2012 at 12:28 AM, Asma Abro 28-FBAS/MSBI/F09 <
> asma.msbi28.iiu.edu.pk> wrote:
>
> > Hi,
> >
> > I am still getting the same error even after replacing the forward slash
> > with &end. Any other suggestions from anyone please...
> >
> > Asma
> >
> > On Tue, Jun 5, 2012 at 4:18 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> >
> > > Hi,
> > >
> > > Try replacing the forward slash with '&end' and see if that works.
> > >
> > > -Dan
> > >
> > > On Tue, Jun 5, 2012 at 3:37 AM, Asma Abro 28-FBAS/MSBI/F09
> > > <asma.msbi28.iiu.edu.pk> wrote:
> > > > Yeah, it's not the problem.
> > > > I am posting the file here:
> > > >
> > > > Mini input
> > > >
> > > > &cntrl
> > > > imin=1, maxcyc = 200, ncyc = 50,
> > > > ntb = 0, igb = 1, cut = 10,
> > > > ntpr = 100
> > > > /
> > > >
> > > > Regards
> > > >
> > > > On Tue, Jun 5, 2012 at 12:26 PM, Ben Roberts <ben.roberts.geek.nz>
> > > wrote:
> > > >
> > > >> Hi Asma,
> > > >>
> > > >> (answer below)
> > > >>
> > > >> On 5/06/2012, at 6:24 PM, Asma Abro 28-FBAS/MSBI/F09 wrote:
> > > >>
> > > >> > Hi all,
> > > >> >
> > > >> > When I am trying to minimize my pdb structure, I am getting the
> > error:
> > > >> >
> > > >> > At line 901 of file _mdread.f (unit = 5, file = 'min.in')
> > > >> > Fortran runtime error: End of file
> > > >> >
> > > >> > Can anyone tell what does this mean?
> > > >>
> > > >> My guess is that it means your input file, which you say is called "
> > > min.in",
> > > >> has been cut short in some way, probably because you forgot to
> > include a
> > > >> final line containing only a forward slash (/). If that's not the
> > > problem,
> > > >> please post the entire min.in to this list so we can better advise
> > you.
> > > >>
> > > >> Regards,
> > > >> Ben
> > > >>
> > > >>
> > > >> _______________________________________________
> > > >> 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
> > >
> > >
> > >
> > > --
> > > -------------------------
> > > Daniel R. Roe, PhD
> > > Lab Specialist
> > > Department of Medicinal Chemistry
> > > University of Utah
> > > 30 South 2000 East, Room 201
> > > Salt Lake City, UT 84112-5820
> > > http://home.chpc.utah.edu/~cheatham/
> > > (801) 587-9652
> > > (801) 585-9119 (Fax)
> > >
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> > >
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Wed Jun 06 2012 - 21:30:04 PDT
