AMBER Archive (2006)

Subject: Re: AMBER: Amber crashed due to power surge and giving problems..

From: Gobind Bisht (gsbisht1_at_gmail.com)
Date: Tue Jul 11 2006 - 12:13:36 CDT

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_at_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>
> >
> > | 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,
>
>
> -----------------------------------------------------------------------
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> 

-- 
Gobind Singh Bisht
Department Of Biotechnology
IIT Kharagpur, Kharagpur-721302
West Bengal,

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