Sat Oct 15 13:42:33 PDT 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 Sat Oct 15 2011 at 13:42:33 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3070 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5062355 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): 2.162000 68.31900 ymin,ymax (A): 42.02800 112.3510 zmin,zma (A): 27.28500 83.39500 x,y,z range (A): 66.15700 70.32300 56.11000 scale (grids/A): 0.5062355 object centre (A): 35.24050 77.18950 55.34000 number of atom coordinates read : 3070 total number of charged atoms : 2891 net assigned charge : -7.999983 assigned positive charge : 462.5956 centred at (gu) : 88.34430 87.81352 90.52908 assigned negative charge : -470.5969 centred at (gu) : 88.42931 87.88800 90.33510 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5277 nv = 96 ne = 84 npr = 56613 no. pairs analyzed = 56613 no. exposed pairs = 4602 no. arc points = 34290 no. surface atoms = 1525 nbur = 1545 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.680000 m= 194 mr = 2199 m= 0 mr = 3 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.2200000 number of dielectric boundary points 3269 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3267 ## 512 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 6960 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.2809844E-10 1.9306137E-10 midg,1,midg; midg,igrid,midg 1.3543586E-11 -1.1521775E-10 1,midg,midg; igrid,midg,midg 3.3488837E-11 -1.4186356E-10 gauss-seidel spectral radius is 0.9799491 estimated iterations to convergence 58 setup time was (sec) 0.4200000 now iterating at: 13:42:34 rms-change max change #iterations 5.0610721E-02 10.72066 at 10iterations 2.7425624E-03 0.4720078 at 20iterations 1.5715342E-04 2.7191162E-02 at 30iterations 1.0274872E-05 2.1209717E-03 at 40iterations 8.7520903E-07 2.1553040E-04 at 50iterations finished qdiffx linear iterations at : 13:42:38 total time elapsed so far: 3.520000 # loops : 50 mean,max change (kT/e) : 8.7520903E-07 2.1553040E-04 energy calculations done at 3.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.650000 DelPhi exited at 13:42:39 3.658u 0.208s 0:05.85 65.8% 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 Sat Oct 15 2011 at 13:42:39 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3070 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.518707 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): 2.162000 68.31900 ymin,ymax (A): 42.02800 112.3510 zmin,zma (A): 27.28500 83.39500 x,y,z range (A): 66.15700 70.32300 56.11000 scale (grids/A): 1.518707 object centre (A): 35.24050 77.18950 55.34000 number of atom coordinates read : 3070 total number of charged atoms : 2891 net assigned charge : -7.999983 assigned positive charge : 462.5956 centred at (gu) : 85.03190 83.43966 91.58638 assigned negative charge : -470.5969 centred at (gu) : 85.28767 83.66367 91.00507 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 58218 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34290 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 15227 mr = 34850 m= 1317 mr = 9156 m= 28 mr = 499 m= 0 mr = 2 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 495 time to turn everything in is 0.3100000 number of dielectric boundary points 30283 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 437 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 21595 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) : 0.5062355 object centre at (A) : 35.24050 77.18950 55.34000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.2683081E-03 7.8153517E-03 midg,1,midg; midg,igrid,midg 3.2134049E-03 -1.6379564E-03 1,midg,midg; igrid,midg,midg -4.4080494E-03 -1.2405870E-02 gauss-seidel spectral radius is 0.9979222 estimated iterations to convergence 174 setup time was (sec) 0.5600000 now iterating at: 13:42:40 rms-change max change #iterations 2.899297 143.2510 at 10iterations 1.127014 55.68336 at 20iterations 0.4389867 19.41978 at 30iterations 0.1713186 6.647368 at 40iterations 6.6702403E-02 2.650135 at 50iterations 2.6062692E-02 1.113918 at 60iterations 1.0198884E-02 0.4173050 at 70iterations 3.9822878E-03 0.1565151 at 80iterations 1.5600397E-03 6.2404633E-02 at 90iterations 6.1155611E-04 2.4847031E-02 at 100iterations 2.3974413E-04 1.0078430E-02 at 110iterations 9.4455208E-05 4.2319298E-03 at 120iterations finished qdiffx linear iterations at : 13:42:52 total time elapsed so far: 8.540000 # loops : 120 mean,max change (kT/e) : 9.4455208E-05 4.2319298E-03 energy calculations done at 8.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.680000 DelPhi exited at 13:42:53 8.679u 0.237s 0:14.19 62.7% 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 Sat Oct 15 2011 at 13:42:53 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3070 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.278060 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): 2.162000 68.31900 ymin,ymax (A): 42.02800 112.3510 zmin,zma (A): 27.28500 83.39500 x,y,z range (A): 66.15700 70.32300 56.11000 scale (grids/A): 2.278060 object centre (A): 35.24050 77.18950 55.34000 number of atom coordinates read : 3070 total number of charged atoms : 2891 net assigned charge : -7.999983 assigned positive charge : 462.5956 centred at (gu) : 82.54762 80.15928 92.37966 assigned negative charge : -470.5969 centred at (gu) : 82.93125 80.49549 91.50741 start vw surface at 0.1000000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 135384 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34290 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 53824 mr = 86844 m= 13248 mr = 38988 m= 1774 mr = 8965 m= 60 mr = 946 m= 3 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 1655 time to turn everything in is 0.7500000 number of dielectric boundary points 68539 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 54 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 23046 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) : 1.518707 object centre at (A) : 35.24050 77.18950 55.34000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1903923 0.1211810 midg,1,midg; midg,igrid,midg 0.1115493 -7.8300245E-02 1,midg,midg; igrid,midg,midg 2.1589827E-03 -0.2407593 gauss-seidel spectral radius is 0.9990584 estimated iterations to convergence 258 setup time was (sec) 1.000000 now iterating at: 13:42:55 rms-change max change #iterations 8.056550 275.9398 at 10iterations 4.481797 164.8952 at 20iterations 2.462183 85.18047 at 30iterations 1.342171 39.26884 at 40iterations 0.7289788 18.74809 at 50iterations 0.3933395 9.770969 at 60iterations 0.2116709 5.425231 at 70iterations 0.1139421 3.140682 at 80iterations 6.1242785E-02 1.360054 at 90iterations 3.2855161E-02 0.7757974 at 100iterations 1.7611127E-02 0.4336910 at 110iterations 9.4348229E-03 0.2257433 at 120iterations 5.0449455E-03 0.1137047 at 130iterations 2.7002834E-03 5.8290482E-02 at 140iterations 1.4452750E-03 3.2303810E-02 at 150iterations 7.7586796E-04 1.7015219E-02 at 160iterations 4.1525243E-04 9.2582703E-03 at 170iterations 2.2289291E-04 5.1057935E-03 at 180iterations finished qdiffx linear iterations at : 13:43:16 total time elapsed so far: 13.62000 # loops : 180 mean,max change (kT/e) : 2.2289291E-04 5.1057935E-03 energy calculations done at 13.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.74000 DelPhi exited at 13:43:19 13.743u 0.301s 0:25.37 55.3% 0+0k 0+0io 0pf+0w