AMBER Archive (2005)

Subject: AMBER: segmentation fault in sander

From: Kenley Barrett (kenley.barrett_at_gmail.com)
Date: Mon Jun 06 2005 - 17:07:59 CDT

Dear Amber users,

I am trying to run a job on Sander which crashes immediately due to a
"Segmentation fault". Does anyone have any idea what might be causing
this? I have pasted the command and the output file below.

Thanks in advance for your help.

Best wishes,
Kenley

$ sander -O -i act_min.in -o act_min.out -p act3.prmtop -c act3.prmcrd
-r act3.rst -cpin act3.cpin -cpout act3.cpout -cprestrt act3.cprestrt
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
sander 080AE58A Unknown Unknown Unknown
sander 080B45A7 Unknown Unknown Unknown
sander 0807990F Unknown Unknown Unknown
sander 08078692 Unknown Unknown Unknown
sander 0804A888 Unknown Unknown Unknown
libc.so.6 00B5578A Unknown Unknown Unknown
sander 0804A741 Unknown Unknown Unknown

         -------------------------------------------------------
          Amber 8 SANDER Scripps/UCSF 2004
          -------------------------------------------------------
 
| Run on 06/06/2005 at 16:39:25
  [-O]verwriting output
 
File Assignments:
| MDIN: act_min.in
| MDOUT: act_min.out
|INPCRD: act3.prmcrd
| PARM: act3.prmtop
|RESTRT: act3.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip
 
                                                                                
 Here is the input file:
  
actin constant pH minimization
                                                                                
&cntrl
imin = 1,
maxcyc = 500,
ntwx = 50,
ntb = 0,
cut = 30,
igb = 2,
saltcon = 0.1,
dt = 0.002,
nrespa = 1,
tempi = 300.0,
temp0 = 300.0,
tautp = 2.0,
gbsa = 1,
ntt = 1,
ntc = 2,
ntf = 2,
tol = 0.000001,
icnstph=1,
solvph=7.2
/
 
--------------------------------------------------------------------------------
  1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
| New format PARM file being parsed.
| Version = 1.000 Date = 06/06/05 Time = 14:17:35
 NATOM = 7958 NTYPES = 19 NBONH = 3958 MBONA = 4082
 NTHETH = 9000 MTHETA = 5534 NPHIH = 16866 MPHIA = 9778
 NHPARM = 0 NPARM = 0 NNB = 43861 NRES = 517
 NBONA = 4082 NTHETA = 5534 NPHIA = 9778 NUMBND = 60
 NUMANG = 133 NPTRA = 63 NATYP = 37 NPHB = 0
 IFBOX = 0 NMXRS = 43 IFCAP = 0 NEXTRA = 0
 NCOPY = 0
 
 
| Memory Use Allocated
| Real 343771
| Hollerith 48267
| Integer 746954
| Max Pairs 1
| Max Rstack 1
| Max Istack 1
| Total 5792 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 = 50, ntrx = 1, ntwr = 500
     iwrap = 0, ntwx = 50, ntwv = 0, ntwe = 0
     ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0
 
Potential function:
     ntf = 2, ntb = 0, igb = 2, nsnb = 25
     ipol = 0, gbsa = 1, iesp = 0
     dielc = 1.00000, cut = 30.00000, intdiel = 1.00000
     saltcon = 0.10000, offset = 0.09000, gbalpha= 0.80000
     gbbeta = 0.00000, gbgamma = 2.90912, surften = 0.00500
     rdt = 0.00000, rgbmax = 25.00000
     scnb = 2.00000, scee = 1.20000
 
Frozen or restrained atoms:
     ibelly = 0, ntr = 0
 
Energy minimization:
     maxcyc = 500, ncyc = 10, ntmin = 1
     dx0 = 0.01000, drms = 0.00010
 
SHAKE:
     ntc = 2, jfastw = 0
     tol = 0.00000
 
Constant pH options:
     ntcnstph = 10
     solvph = 7.20000
reading charge increments from file: act3.cpin
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