AMBER Archive (2009)

Subject: Re: [AMBER] Error in MM PBSA

From: Vikas Sharma (vs_vikassharma_at_yahoo.co.in)
Date: Sat Jun 06 2009 - 04:03:22 CDT

Dear Dr. Ray Luo,

Sorry for replying so late...actualyy i checked the output file, found an erro..rectified it and re-ran the command:

mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log

i got the follwing error:

 /opt/amber10/exe/sander -O -i pbsa_com.in -o pb sa_com.7.out -c /home/bharatam/amberresults_w/amberresults31/snapshot_com.crd.7 -p /home/bha ratam/amberresults_w/amb31/A31.prmtop not successful

 
the contents of the output file are pasted below:
          -------------------------------------------------------
          Amber 10 SANDER                              2008
          -------------------------------------------------------

| Run on 06/05/2009 at 15:43:50
  [-O]verwriting output

File Assignments:
|  MDIN: pbsa_com.in                                                          
| MDOUT: pbsa_com.7.out                                                       
|INPCRD: /home/bharatam/amberresults_w/amberresults31/snapshot_com.crd.7      
|  PARM: /home/bharatam/amberresults_w/amb31/A31.prmtop                       
|RESTRT: restrt                                                               
|  REFC: refc                                                                 
| MDVEL: mdvel                                                                 
|  MDEN: mden                                                                 
| MDCRD: mdcrd                                                                
|MDINFO: mdinfo                                                                
|INPDIP: inpdip                                                               
|RSTDIP: rstdip                                                               

|INPTRA: inptraj                                                               
|
 
 Here is the input file:
 
File generated by mm_pbsa.pl. Using PB                                        
 &cntrl                                                                       
  ntf    = 1,       ntb    = 0,                                                
  igb    = 10,      dielc  = 1.0,                                             
  cut    = 999.0,   nsnb   = 99999,                                           
  scnb   = 2.0,     scee   = 1.2,                                              
  imin   = 1,       maxcyc = 0,       ntmin  = 2,                             
  ivcap  = 0,       cutcap = -1,                                              
  xcap   = 0, ycap   = 0, zcap   = 0                                           
  idecomp= 0,                                                                 
 &end                                                                         
 &pb                                                                          
  epsin  = 1.0,     epsout  = 80.0,                                           
  istrng = 0.0,       radiopt = 0,                                            
  sprob  = 1.4,     space   = 0.5,                                            
  maxitn = 1000,    npopt   = 1,    dbfopt  = 1,                              
  cavity_surften = 0.0072,    cavity_offset   = 0.00,                         
  pbtemp    = 300.0,                                                          
  fillratio = 4.0   npbverb= 1                                                 
 &end                                                                         

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

| Flags:                                                                       
| New format PARM file being parsed.
| Version =    1.000 Date = 05/25/09 Time = 15:24:22
 NATOM  =    3777 NTYPES =      14 NBONH =    1904 MBONA  =    1908
 NTHETH =    4330 MTHETA =    2563 NPHIH =    8175 MPHIA  =    5873
 NHPARM =       0 NPARM  =       0 NNB   =   20879 NRES   =     224
 NBONA  =    1908 NTHETA =    2563 NPHIA =    5873 NUMBND =      52
 NUMANG =     108 NPTRA  =      51 NATYP =      39 NPHB   =       0
 IFBOX  =       0 NMXRS  =      44 IFCAP =       0 NEXTRA =       0
 NCOPY  =       0

 Implicit solvent radii are modified Bondi radii (mbondi)                                                  

|     Memory Use     Allocated
|     Real              242174
|     Hollerith          22888
|     Integer           213271
|     Max Pairs              1
|     nblistReal             0
|     nblist Int             0
|       Total             2814 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    =       0, ntwv    =       0, ntwe    =       0
     ioutfm  =       0, ntwprt  =       0, idecomp =       0, rbornstat=      0

Potential function:
     ntf     =       1, ntb     =       0, igb     =      10, nsnb    =   99999
     ipol    =       0, gbsa    =       0, iesp    =       0
     dielc   =   1.00000, cut     = 999.00000, intdiel =   1.00000
     scnb    =   2.00000, scee    =   1.20000

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

Energy minimization:
     maxcyc  =       0, ncyc    =      10, ntmin   =       2
     dx0     =   0.01000, drms    =   0.00010
 
 ======== Implicit Solvent Initialization ========
 
     Max Nonbonded Pairs:  4249125   917811  7132865
 
  no. of atoms processed in PB initialization:        3777
  NUM  RESI  NAME  TYPE    CHARGE ATM CRG/H   GRP CRG   PB RADI   NP RADI
    1  MET   N     N3    0.159200  0.754400  0.888100  1.550000  1.550000
    2  MET   H1    H     0.198400  0.000000  0.000000  1.300000  1.300000
....
...
....
....
....
....
....3741  M_4   C2    c3    0.167121  0.155371 -0.079574  1.700000  1.700000
 3742  M_4   H2    hc   -0.005875 -0.005875 -0.005875  1.300000  1.300000
 3743  M_4   H15   hc   -0.005875 -0.005875 -0.005875  1.300000  1.300000
 3744  M_4   C4    ca   -0.078846 -0.078846  0.144835  1.700000  1.700000
 3745  M_4   C9    ca   -0.107028  0.034155 -0.192893  1.700000  1.700000
 3746  M_4   C8    ca   -0.321534 -0.148202  0.293820  1.700000  1.700000
 3747  M_4   H3    ha    0.173332  0.173332  0.173332  1.300000  1.300000
 3748  M_4   H6    ha    0.141183  0.141183  0.141183  1.300000  1.300000
 3749  M_4   C5    ca   -0.107028  0.034155 -0.192893  1.700000  1.700000
 3750  M_4   H5    ha    0.141183  0.141183  0.141183  1.300000  1.300000
 3751  M_4   C6    ca   -0.321534 -0.148202  0.293820  1.700000  1.700000
 3752  M_4   H4    ha    0.173332  0.173332  0.173332  1.300000  1.300000
 3753  M_4   C7    ca    0.407867  0.407867 -0.274762  1.700000  1.700000
 3754  M_4   O3    os   -0.386225 -0.386225  0.268150  1.500000  1.500000
 3755  M_4   C16   c3    0.216240  0.246508 -0.191950  1.700000  1.700000
 3756  M_4   H19   h1    0.015134  0.015134  0.015134  1.300000  1.300000
 3757  M_4   H20   h1    0.015134  0.015134  0.015134  1.300000  1.300000
 3758  M_4   C15   c3   -0.202531 -0.052233  0.539870  1.700000  1.700000
 3759  M_4   H14   hc    0.075149  0.075149  0.075149  1.300000  1.300000
 3760  M_4   H18   hc    0.075149  0.075149  0.075149  1.300000  1.300000
 3761  M_4   C14   c3    0.362373  0.345595 -0.134888  1.700000  1.700000
 3762  M_4   H8    h1   -0.008389 -0.008389 -0.008389  1.300000  1.300000
 3763  M_4   H9    h1   -0.008389 -0.008389 -0.008389  1.300000  1.300000
 3764  M_4   O4    os   -0.428250 -0.428250 -0.329184  1.500000  1.500000
 3765  M_4   C11   ca   -0.246529 -0.246529  0.593314  1.700000  1.700000
 3766  M_4   C10   ca    0.315820  0.448944 -0.600706  1.700000  1.700000
 3767  M_4   H7    h4    0.133124  0.133124  0.133124  1.300000  1.300000
 3768  M_4   N1    nb   -0.803121 -0.803121  0.693260  1.550000  1.550000
 3769  M_4   C12   ca    1.047437  1.047437 -0.763398  1.700000  1.700000
 3770  M_4   N3    nh   -0.974766 -0.177972  0.869465  1.550000  1.550000
 3771  M_4   H10   hn    0.398397  0.398397  0.398397  1.300000  1.300000
 3772  M_4   H11   hn    0.398397  0.398397  0.398397  1.300000  1.300000
 3773  M_4   N2    nb   -0.829742 -0.829742  1.036844  1.550000  1.550000
 3774  M_4   C13   ca    0.819149  0.819149 -0.390502  1.700000  1.700000
 3775  M_4   N4    nh   -0.956186 -0.133380  0.685769  1.550000  1.550000
 3776  M_4   H12   hn    0.411403  0.411403  0.411403  1.300000  1.300000
 3777  M_4   H13   hn    0.411403  0.411403  0.411403  1.300000  1.300000
 
 total system charges (+/-) for PB        9.0000      420.3270     -411.3270
 cavity_surften =        0.0072 cavity_offset =        0.0000
 
  SAS Surface: surface dots generated:    366
|  INFO: Old style inpcrd file read

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

                                                                               
 begin time read from input coords =     0.000 ps

 Number of triangulated 3-point waters found:        0

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

  NB-update: residue-based nb list  1383768
  NB-update: atom-based nb list    53172
 
 
 ======== Setting up Grid Parameters ========
 Using bounding box for grid setup
 Bounding Box Center:      47.000    43.500    29.000
 Xmin, Xmax, Xmax-Xmin:    -6.933   100.641   107.574
 Ymin, Ymax, Ymax-Ymin:   -18.558   105.341   123.899
 Zmin, Zmax, Zmax-Zmin:   -29.798    88.266   118.064
   beginning box center at level      1     47.000    43.500    29.000
   beginning box center at level      2     47.000    43.500    29.000
 Grid dimension at level     1   109  125  119
 Grid origin corrected at level     1   -173.000  -208.500  -211.000
 Grid dimension at level     2   229  263  251
 Grid origin corrected at level     2    -10.500   -22.500   -34.000
  SA surface: setting up working radii
  SA surface: found nonzero radii        3777
Number of SA srf points exposed455488
 SA Bomb in sa_arc(): Allocation aborted           0           0          41
           0           0

 

 Vikas Sharma (+91-9780449303)
Molecular Modeling lab.
Department of Medicinal Chemistry
National Institute of Pharmaceutical Education & Research (NIPER),
SAS Nagar, Mohali,
Punjab (INDIA)

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

      Bollywood news, movie reviews, film trailers and more! Go to http://in.movies.yahoo.com/
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber