AMBER Archive (2006)

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

From: Gobind Bisht (gsbisht1_at_gmail.com)
Date: Tue Jul 11 2006 - 09:46:54 CDT


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

| 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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