i once more recreated the inpcrd file and it worked now. I don't know why it
behaved in this weird way before. anyway thanx a lot for help.
gobind
On 7/12/06, Carlos Simmerling <carlos.csb.sunysb.edu> wrote:
>
> I don't really understand what's going on- did this work before
> the crash? if you regenerated the input and did exactly the same thing
> as before it's hard to understand why Amber wouldn't work just like
> it did before. Something must be missing- are you sure that the inpcrd
> is in the correct directory?
>
> Gobind Bisht wrote:
>
> > hi carlos,
> > I regenerated it. but it's still giving the same error. This
> > error is with the regenerated file only.
> >
> > On 7/11/06, *Carlos Simmerling* <carlos.csb.sunysb.edu
> > <mailto:carlos.csb.sunysb.edu>> wrote:
> >
> > does the aptase_neutral.inpcrd file exist? if yes, is it corrupted?
> > if it is gone or corrupt you need to restore it from
> > your backup or else generate it again.
> >
> > Gobind Bisht wrote:
> >
> > > Hi all,
> > > I was running a minimisation on AMBER9 in windows using
> > cygwin
> > > and the computer went off due to a power surge while the job was
> > > running. Now when i'm trying to run it again it's giving the
> > following
> > > problem. What should I do? Please help...
> > >
> >
> ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
> >
> > >
> > > -------------------------------------------------------
> > > Amber 9 SANDER 2006
> > > -------------------------------------------------------
> > >
> > > | Run on 07/11/2006 at 20:02:28
> > > [-O]verwriting output
> > >
> > > File Assignments:
> > > | MDIN: min1.in <http://min1.in>
> > > <http://min1.in >
> > >
> > > | MDOUT:
> > > min4.out
> > > |INPCRD:
> > > aptase_neutral.inpcrd
> > > | PARM:
> > > atpase_neutral.prmtop
> > > |RESTRT:
> > > min4.rst
> > > | REFC:
> > > refc
> > > | MDVEL:
> > > mdvel
> > > | MDEN:
> > > mden
> > > | MDCRD:
> > > mdcrd
> > > |MDINFO:
> > > mdinfo
> > > |INPDIP:
> > > inpdip
> > > |RSTDIP:
> > > rstdip
> > >
> > >
> > > Here is the input file:
> > >
> > > minimisation run for
> > > F1ATpase
> > > &cntrl
> > >
> > > imin =
> > > 1,
> > >
> > > ntpr=5,
> > >
> > > maxcyc
> > > =500,
> > > ncyc =
> > > 250,
> > > ntb =
> > > 0,
> > >
> > > igb=1,
> > >
> > > ntr =
> > > 0,
> > > cut =
> > > 10,
> > > /
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> >
> --------------------------------------------------------------------------------
> >
> > >
> > > 1. RESOURCE USE:
> > >
> >
> --------------------------------------------------------------------------------
> > >
> > > |
> > > Flags:
> > >
> > > | New format PARM file being parsed.
> > > | Version = 1.000 Date = 07/11/06 Time = 19:58:22
> > > NATOM = 49825 NTYPES = 21 NBONH = 25164 MBONA =
> 24977
> > > NTHETH = 57073 MTHETA = 33827 NPHIH = 107156 MPHIA =
> 66222
> > > NHPARM = 0 NPARM = 0 NNB = 274472 NRES
> = 3290
> > > NBONA = 24977 NTHETA = 33827 NPHIA = 66222 NUMBND
> = 60
> > > NUMANG = 125 NPTRA = 61 NATYP = 42 NPHB =
> 1
> > > IFBOX = 0 NMXRS = 43 IFCAP = 0 NEXTRA =
> 0
> > > NCOPY = 0
> > >
> > > Implicit solvent radii are modified Bondi radii
> > > (mbondi)
> > >
> > > | Memory Use Allocated
> > > | Real 3190341
> > > | Hollerith 302242
> > > | Integer 2505589
> > > | Max Pairs 1
> > > | nblistReal 0
> > > | nblist Int 0
> > > | Total 35892 kbytes
> > > | Duplicated 0 dihedrals
> > > | Duplicated 0 dihedrals
> > >
> > >
> >
> --------------------------------------------------------------------------------
> > > 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 = 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
> > > alpb = 0
> > > scnb = 2.00000, scee = 1.20000
> > >
> > > Frozen or restrained atoms:
> > > ibelly = 0, ntr = 0
> > >
> > > Energy minimization:
> > > maxcyc = 500, ncyc = 250, ntmin = 1
> > > dx0 = 0.01000 , drms = 0.00010
> > >
> > > Unit 30 Error on OPEN:
> > > aptase_neutral.inpcrd
> > >
> > >
> > > --
> > >
> >
> -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
> >
> > > Gobind Singh Bisht
> > > Department Of Biotechnology
> > > IIT Kharagpur, Kharagpur-721302
> > > West Bengal,
> >
> >
> >
> -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber.scripps.edu <mailto:amber.scripps.edu>
> > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> > <mailto:majordomo.scripps.edu>
> >
> >
> >
> >
> > --
> > Gobind Singh Bisht
> > Department Of Biotechnology
> > IIT Kharagpur, Kharagpur-721302
> > West Bengal,
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
--
Gobind Singh Bisht
Department Of Biotechnology
IIT Kharagpur, Kharagpur-721302
West Bengal,
-----------------------------------------------------------------------
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Received on Wed Jul 12 2006 - 06:07:19 PDT
