[AMBER] Segmentation fault

From: Asfa Ali <asfa.iisc.gmail.com>
Date: Wed, 3 Mar 2010 20:50:28 +0530

Dear Sir,
I have problem on segmentation fault when I am running the minimization of
duplex DNA-ligand complex. I have generated my small duplex DNA by using
nucgen, and I have done minimization and MD simulation on this structure.
and then I am taking the minimized duplex DNA structure and doing docking
with my ligand by using autodock 4. After docking i am taking this
DNA-ligand complex for the minimization and simulation. To generate the
parameter file of ligand i am using Antechamber. During antechamber running
some information is coming like Info:the number of the path atoms exceeds
MAXPATHATOMNUM(number)for atom (36)....(122), extend the size and rellocate
the memory automatically.
But it is generating the antechamber out put file and ligand prepin and
frcmod file. Taking these file I am generating DNA-ligand complex prmtop and
inpcrd file by using leap, I am attaching leap.log file, here some warnings
I am getting
Taking all these promtop and inpcrd file i am submitting for first step
minimization and getting segmentation fault. and the out put file is like
this
| Run on 03/03/2010 at 19:33:14
  [-O]verwriting output

File Assignments:
| MDIN: dlcmin1.in

| MDOUT:
dlcmin1.out
|INPCRD:
dlc.inpcrd
| PARM:
dlc.prmtop
|RESTRT:
dlcmin1.rst
| REFC:
dlc.inpcrd
| MDVEL:
mdvel
| MDEN:
mden
| MDCRD:
mdcrd
|MDINFO:
mdinfo
|INPDIP:
inpdip
|RSTDIP:
rstdip

|INPTRA:
inptraj
|

 Here is the input file:

initial minimization solvent +
ions
&cntrl

imin =
1,
maxcyc =
2000,
ntb =
1,
ntr =
1,
cut =
10.0
/

Hold the DNA
fixed
500.0

RES 1
32
END

END


--------------------------------------------------------------------------------
   1. RESOURCE USE:
--------------------------------------------------------------------------------

|
Flags:

 getting new box info from bottom of inpcrd
| INFO: Old style inpcrd file read

| peek_ewald_inpcrd: Box info found
|Largest sphere to fit in unit cell has radius = 30.408
| New format PARM file being parsed.
| Version = 1.000 Date = 03/03/10 Time = 19:29:50
 NATOM = 27957 NTYPES = 18 NBONH = 27205 MBONA = 811
 NTHETH = 1005 MTHETA = 1238 NPHIH = 2067 MPHIA = 2186
 NHPARM = 0 NPARM = 0 NNB = 42109 NRES = 8989
 NBONA = 811 NTHETA = 1238 NPHIA = 2186 NUMBND = 54
 NUMANG = 103 NPTRA = 48 NATYP = 39 NPHB = 1
 IFBOX = 2 NMXRS = 130 IFCAP = 0 NEXTRA = 0
 NCOPY = 0


| Memory Use Allocated
| Real 1873671
| Hollerith 176733
| Integer 710451
| Max Pairs 16103232
| nblistReal 335484
| nblist Int 937045
| Total 87288 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals

     BOX TYPE: TRUNCATED OCTAHEDRON

--------------------------------------------------------------------------------
   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 = 0, ntwv = 0, ntwe
= 0
     ioutfm = 0, ntwprt = 0, idecomp = 0,
rbornstat= 0

Potential function:
     ntf = 1, ntb = 1, igb = 0, nsnb =
25
     ipol = 0, gbsa = 0, iesp = 0
     dielc = 1.00000, cut = 10.00000, intdiel = 1.00000
     scnb = 2.00000, scee = 1.20000

Frozen or restrained atoms:
     ibelly = 0, ntr = 1

Energy minimization:
     maxcyc = 2000, ncyc = 10, ntmin = 1
     dx0 = 0.01000, drms = 0.00010

Ewald parameters:
     verbose = 0, ew_type = 0, nbflag = 1, use_pme
= 1
     vdwmeth = 1, eedmeth = 1, netfrc = 0
     Box X = 74.485 Box Y = 74.485 Box Z = 74.485
     Alpha = 109.471 Beta = 109.471 Gamma = 109.471
     NFFT1 = 80 NFFT2 = 75 NFFT3 = 75
     Cutoff= 10.000 Tol =0.100E-04
     Ewald Coefficient = 0.27511
     Interpolation order = 4

    LOADING THE CONSTRAINED ATOMS AS GROUPS


   5. REFERENCE ATOM COORDINATES


    ----- READING GROUP 1; TITLE:
 Hold the DNA fixed


     GROUP 1 HAS HARMONIC CONSTRAINTS 500.00000
 GRP 1 RES 1 TO 32
      Number of atoms in this group = 1019
    ----- END OF GROUP READ -----

--------------------------------------------------------------------------------
   3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------



 begin time read from input coords = 0.000 ps

 Number of triangulated 3-point waters found: 8926

     Sum of charges from parm topology file = 0.00000015
     Forcing neutrality...

--------------------------------------------------------------------------------
   4. RESULTS
--------------------------------------------------------------------------------

 ---------------------------------------------------
 APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
 using 5000.0 points per unit in tabled values
 TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.3328E-14 at 2.473100
| CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960
 ---------------------------------------------------
| Local SIZE OF NONBOND LIST = 8901285
| TOTAL SIZE OF NONBOND LIST = 8901285


   NSTEP ENERGY RMS GMAX NAME NUMBER
      1 9.4604E+09 1.5560E+09 2.7921E+11 H32 1126

 BOND = 1696.8908 ANGLE = 2066.7149 DIHED =
732.6391
 VDWAALS = 10803.9961 EEL = -92062.0905 HBOND =
0.0000
 1-4 VDW = ************* 1-4 EEL = -1609.5457 RESTRAINT =
0.0000

Please suggest me how I will solve this problem
Thank you
With regards
Asfa.


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Received on Wed Mar 03 2010 - 07:30:02 PST
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