Mon Oct 10 14:12:26 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 Mon Oct 10 2011 at 14:12:26 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2106 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 0.6373304 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): -13.21400 41.04000 ymin,ymax (A): -31.96400 23.89400 zmin,zma (A): -9.653001 32.62100 x,y,z range (A): 54.25400 55.85800 42.27400 scale (grids/A): 0.6373304 object centre (A): 13.91300 -4.035000 11.48400 number of atom coordinates read : 2106 total number of charged atoms : 1974 net assigned charge : 11.51402 assigned positive charge : 305.8969 centred at (gu) : 88.66109 91.80162 91.69111 assigned negative charge : -294.3833 centred at (gu) : 88.68707 91.87022 91.65799 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6101 nv = 96 ne = 84 npr = 41206 no. pairs analyzed = 41206 no. exposed pairs = 2869 no. arc points = 20570 no. surface atoms = 965 nbur = 1141 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 376 mr = 3133 m= 2 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3309 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2051 ## 179 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 7065 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.0202983E-09 2.5880054E-08 midg,1,midg; midg,igrid,midg 1.4412660E-08 1.4090237E-08 1,midg,midg; igrid,midg,midg 2.3233927E-08 1.0120149E-08 gauss-seidel spectral radius is 0.9872147 estimated iterations to convergence 72 setup time was (sec) 0.5100000 now iterating at: 14:12:27 rms-change max change #iterations 0.1226087 21.59153 at 10iterations 1.2040572E-02 2.169386 at 20iterations 1.2215310E-03 0.1897650 at 30iterations 1.7834894E-04 2.7868271E-02 at 40iterations 4.2822641E-05 6.8397522E-03 at 50iterations finished qdiffx linear iterations at : 14:12:30 total time elapsed so far: 3.860000 # loops : 50 mean,max change (kT/e) : 4.2822641E-05 6.8397522E-03 energy calculations done at 3.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.040000 DelPhi exited at 14:12:31 4.042u 0.235s 0:04.93 86.6% 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 Mon Oct 10 2011 at 14:12:31 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2106 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 1.911991 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): -13.21400 41.04000 ymin,ymax (A): -31.96400 23.89400 zmin,zma (A): -9.653001 32.62100 x,y,z range (A): 54.25400 55.85800 42.27400 scale (grids/A): 1.911991 object centre (A): 13.91300 -4.035000 11.48400 number of atom coordinates read : 2106 total number of charged atoms : 1974 net assigned charge : 11.51402 assigned positive charge : 305.8969 centred at (gu) : 85.98317 95.40477 95.07303 assigned negative charge : -294.3833 centred at (gu) : 86.06148 95.61085 94.97392 start vw surface at 0.1400000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 64940 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20570 grid for indexing accessible points = 1.400000 m= 24125 mr = 43211 m= 4256 mr = 17465 m= 275 mr = 2656 m= 2 mr = 100 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 30166 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 152 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 15544 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) : 0.6373304 object centre at (A) : 13.91300 -4.035000 11.48400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4659801E-04 2.5726458E-02 midg,1,midg; midg,igrid,midg 3.9574172E-02 3.0474927E-02 1,midg,midg; igrid,midg,midg 5.7232175E-02 3.1332284E-02 gauss-seidel spectral radius is 0.9986031 estimated iterations to convergence 212 setup time was (sec) 0.8300000 now iterating at: 14:12:32 rms-change max change #iterations 3.672448 181.4493 at 10iterations 1.697542 65.78442 at 20iterations 0.7856498 29.38470 at 30iterations 0.3627399 12.71292 at 40iterations 0.1682963 5.921847 at 50iterations 7.8076638E-02 2.614264 at 60iterations 3.6105700E-02 1.435566 at 70iterations 1.6738972E-02 0.5528517 at 80iterations 7.7847480E-03 0.2700748 at 90iterations 3.6164131E-03 0.1219444 at 100iterations 1.6960172E-03 5.7274818E-02 at 110iterations 7.9691131E-04 2.5290966E-02 at 120iterations finished qdiffx linear iterations at : 14:12:40 total time elapsed so far: 9.060000 # loops : 120 mean,max change (kT/e) : 7.9691131E-04 2.5290966E-02 energy calculations done at 9.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.250000 DelPhi exited at 14:12:41 9.251u 0.247s 0:09.83 96.5% 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 Mon Oct 10 2011 at 14:12:41 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2106 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 2.867987 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): -13.21400 41.04000 ymin,ymax (A): -31.96400 23.89400 zmin,zma (A): -9.653001 32.62100 x,y,z range (A): 54.25400 55.85800 42.27400 scale (grids/A): 2.867987 object centre (A): 13.91300 -4.035000 11.48400 number of atom coordinates read : 2106 total number of charged atoms : 1974 net assigned charge : 11.51402 assigned positive charge : 305.8969 centred at (gu) : 83.97464 98.10709 97.60970 assigned negative charge : -294.3833 centred at (gu) : 84.09234 98.41624 97.46088 start vw surface at 0.1400000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 149788 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20570 grid for indexing accessible points = 1.400000 m= 76419 mr = 105032 m= 28960 mr = 61509 m= 7680 mr = 23097 m= 1179 mr = 5751 m= 63 mr = 777 m= 0 mr = 15 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.340000 number of dielectric boundary points 67908 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.490000 number of grid points assigned charge 15792 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) : 1.911991 object centre at (A) : 13.91300 -4.035000 11.48400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0129776E-03 0.2758330 midg,1,midg; midg,igrid,midg 0.4630651 0.3506684 1,midg,midg; igrid,midg,midg 0.5842365 0.2885864 gauss-seidel spectral radius is 0.9992514 estimated iterations to convergence 288 setup time was (sec) 1.700000 now iterating at: 14:12:43 rms-change max change #iterations 8.849675 346.7853 at 10iterations 5.207094 135.4482 at 20iterations 3.037325 77.68846 at 30iterations 1.769799 39.27047 at 40iterations 1.023878 25.87797 at 50iterations 0.5917372 12.22892 at 60iterations 0.3420069 8.153389 at 70iterations 0.1970174 4.341705 at 80iterations 0.1135039 2.386398 at 90iterations 6.5327853E-02 1.373148 at 100iterations 3.7543878E-02 0.8699722 at 110iterations 2.1609869E-02 0.4405231 at 120iterations 1.2414570E-02 0.2664557 at 130iterations 7.1017500E-03 0.1478567 at 140iterations 4.0919408E-03 8.1654310E-02 at 150iterations 2.3569295E-03 4.7006607E-02 at 160iterations 1.3599151E-03 2.6245117E-02 at 170iterations 7.8580133E-04 1.5306950E-02 at 180iterations finished qdiffx linear iterations at : 14:12:57 total time elapsed so far: 15.58000 # loops : 180 mean,max change (kT/e) : 7.8580133E-04 1.5306950E-02 energy calculations done at 15.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.76000 DelPhi exited at 14:12:57 15.763u 0.315s 0:16.39 98.0% 0+0k 0+0io 0pf+0w