AMBER Archive (2006)

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

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Tue Jul 11 2006 - 14:05:48 CDT

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_at_csb.sunysb.edu
> <mailto: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>
> > <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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