Wed Dec 21 14:21:41 PST 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Wed Dec 21 2011 at 14:21:43 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6461684 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -6.337000 35.16200 ymin,ymax (A): -3.807000 49.60000 zmin,zma (A): -24.18800 30.90600 x,y,z range (A): 41.49900 53.40700 55.09400 scale (grids/A): 0.6461684 object centre (A): 14.41250 22.89650 3.359000 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000006 assigned positive charge : 291.8260 centred at (gu) : 90.88740 92.35338 90.20352 assigned negative charge : -289.8262 centred at (gu) : 91.01952 92.50527 90.12443 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5651 nv = 96 ne = 84 npr = 40169 no. pairs analyzed = 40169 no. exposed pairs = 2390 no. arc points = 16877 no. surface atoms = 811 nbur = 1153 mkacc time = 5.9999995E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 308 mr = 3234 m= 0 mr = 47 time to grow re-entrant surface = 7.0000000E-02 no. cavity mid-points inaccessible to solvent = 40 time to turn everything in is 0.1800000 number of dielectric boundary points 2678 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1625 ## 158 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 6496 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.9553041E-09 1.2534142E-08 midg,1,midg; midg,igrid,midg 1.1713147E-08 -1.9894612E-08 1,midg,midg; igrid,midg,midg 1.4316496E-08 -1.1786041E-08 gauss-seidel spectral radius is 0.9875337 estimated iterations to convergence 73 setup time was (sec) 0.3800000 now iterating at: 14:21:43 rms-change max change #iterations 0.1350580 23.91341 at 10iterations 1.3293623E-02 2.056274 at 20iterations 1.3814807E-03 0.2129383 at 30iterations 1.3468515E-04 2.4760723E-02 at 40iterations 1.3767602E-05 2.0484924E-03 at 50iterations finished qdiffx linear iterations at : 14:21:47 total time elapsed so far: 3.800000 # loops : 50 mean,max change (kT/e) : 1.3767602E-05 2.0484924E-03 energy calculations done at 3.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.940000 DelPhi exited at 14:22:02 3.944u 0.228s 0:21.32 19.5% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Wed Dec 21 2011 at 14:22:08 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.938505 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -6.337000 35.16200 ymin,ymax (A): -3.807000 49.60000 zmin,zma (A): -24.18800 30.90600 x,y,z range (A): 41.49900 53.40700 55.09400 scale (grids/A): 1.938505 object centre (A): 14.41250 22.89650 3.359000 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000006 assigned positive charge : 291.8260 centred at (gu) : 92.66222 97.06032 90.61044 assigned negative charge : -289.8262 centred at (gu) : 93.05881 97.51599 90.37360 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 60659 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16877 grid for indexing accessible points = 1.400000 m= 22397 mr = 42240 m= 3449 mr = 17245 m= 222 mr = 2363 m= 4 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 3007 time to turn everything in is 0.3300000 number of dielectric boundary points 24791 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 120 iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 14441 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.6461684 object centre at (A) : 14.41250 22.89650 3.359000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7271626E-02 1.5919382E-02 midg,1,midg; midg,igrid,midg 3.6673449E-02 -1.7487859E-02 1,midg,midg; igrid,midg,midg 1.0465437E-02 -8.2338918E-03 gauss-seidel spectral radius is 0.9986026 estimated iterations to convergence 212 setup time was (sec) 0.5400000 now iterating at: 14:22:11 rms-change max change #iterations 3.739307 168.0673 at 10iterations 1.741507 79.80053 at 20iterations 0.8090140 33.34333 at 30iterations 0.3761071 13.06459 at 40iterations 0.1745853 5.999783 at 50iterations 8.0900639E-02 2.951309 at 60iterations 3.7548192E-02 1.446459 at 70iterations 1.7448457E-02 0.5606165 at 80iterations 8.0598472E-03 0.2836781 at 90iterations 3.7373626E-03 0.1282387 at 100iterations 1.7409901E-03 6.0420513E-02 at 110iterations 8.0917834E-04 2.6412964E-02 at 120iterations finished qdiffx linear iterations at : 14:22:20 total time elapsed so far: 10.04000 # loops : 120 mean,max change (kT/e) : 8.0917834E-04 2.6412964E-02 energy calculations done at 10.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.18000 DelPhi exited at 14:22:24 10.183u 0.265s 0:17.38 60.0% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Wed Dec 21 2011 at 14:22:31 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.907758 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -6.337000 35.16200 ymin,ymax (A): -3.807000 49.60000 zmin,zma (A): -24.18800 30.90600 x,y,z range (A): 41.49900 53.40700 55.09400 scale (grids/A): 2.907758 object centre (A): 14.41250 22.89650 3.359000 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000006 assigned positive charge : 291.8260 centred at (gu) : 93.99329 100.5905 90.91578 assigned negative charge : -289.8262 centred at (gu) : 94.58821 101.2741 90.56043 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 139984 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16877 grid for indexing accessible points = 1.400000 m= 72365 mr = 101931 m= 26428 mr = 60341 m= 6195 mr = 22160 m= 1010 mr = 4957 m= 93 mr = 749 m= 3 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 10376 time to turn everything in is 0.8100000 number of dielectric boundary points 55885 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 14656 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.938505 object centre at (A) : 14.41250 22.89650 3.359000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.016673 3.9719503E-02 midg,1,midg; midg,igrid,midg 0.3737957 -0.2042202 1,midg,midg; igrid,midg,midg 6.4345174E-02 -4.2881217E-02 gauss-seidel spectral radius is 0.9992356 estimated iterations to convergence 285 setup time was (sec) 1.050000 now iterating at: 14:22:36 rms-change max change #iterations 8.699419 401.4445 at 10iterations 4.943471 116.2324 at 20iterations 2.798842 58.32462 at 30iterations 1.589614 34.23598 at 40iterations 0.9057794 18.25873 at 50iterations 0.5145776 11.09784 at 60iterations 0.2919980 5.917549 at 70iterations 0.1654974 3.370377 at 80iterations 9.3819894E-02 1.800770 at 90iterations 5.3272497E-02 1.002796 at 100iterations 3.0285865E-02 0.6140504 at 110iterations 1.7167876E-02 0.3689075 at 120iterations 9.7531695E-03 0.2026396 at 130iterations 5.5453200E-03 0.1197166 at 140iterations 3.1527292E-03 6.1630249E-02 at 150iterations 1.7903143E-03 3.3447266E-02 at 160iterations 1.0166084E-03 2.3853302E-02 at 170iterations 5.7826540E-04 1.1425972E-02 at 180iterations finished qdiffx linear iterations at : 14:22:53 total time elapsed so far: 17.70000 # loops : 180 mean,max change (kT/e) : 5.7826540E-04 1.1425972E-02 energy calculations done at 17.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.84000 DelPhi exited at 14:23:02 17.841u 0.236s 0:31.30 57.7% 0+0k 0+0io 0pf+0w