Sun Oct 9 16:00:24 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 Sun Oct 9 2011 at 16:00:24 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3038 !!! WARNING: GLM 156 has a net charge of -0.0940 !!! WARNING: GLM 225 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6361119 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): -15.20100 37.06100 ymin,ymax (A): 3.634000 56.21900 zmin,zma (A): -34.56200 21.40300 x,y,z range (A): 52.26200 52.58500 55.96500 scale (grids/A): 0.6361119 object centre (A): 10.93000 29.92650 -6.579500 number of atom coordinates read : 3038 total number of charged atoms : 2886 net assigned charge : -5.687977 assigned positive charge : 447.2592 centred at (gu) : 90.49921 91.17613 88.71493 assigned negative charge : -452.9486 centred at (gu) : 90.52834 91.31090 88.66405 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8213 nv = 96 ne = 84 npr = 62696 no. pairs analyzed = 62696 no. exposed pairs = 3726 no. arc points = 26145 no. surface atoms = 1259 nbur = 1779 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 429 mr = 4536 m= 5 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 4053 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2511 ## 217 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 9930 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7489368E-08 -7.4119183E-10 midg,1,midg; midg,igrid,midg 7.0056738E-09 -3.0623625E-08 1,midg,midg; igrid,midg,midg -3.1743455E-09 -1.1781814E-08 gauss-seidel spectral radius is 0.9872361 estimated iterations to convergence 72 setup time was (sec) 0.5300000 now iterating at: 16:00:25 rms-change max change #iterations 0.1565295 22.96441 at 10iterations 1.5439812E-02 1.966072 at 20iterations 1.6375273E-03 0.2370834 at 30iterations 3.1340407E-04 5.7904720E-02 at 40iterations 1.0796413E-04 2.1615982E-02 at 50iterations finished qdiffx linear iterations at : 16:00:27 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 1.0796413E-04 2.1615982E-02 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.120000 DelPhi exited at 16:00:28 3.119u 0.146s 0:03.60 90.2% 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 Sun Oct 9 2011 at 16:00:28 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3038 !!! WARNING: GLM 156 has a net charge of -0.0940 !!! WARNING: GLM 225 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.908336 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): -15.20100 37.06100 ymin,ymax (A): 3.634000 56.21900 zmin,zma (A): -34.56200 21.40300 x,y,z range (A): 52.26200 52.58500 55.96500 scale (grids/A): 1.908336 object centre (A): 10.93000 29.92650 -6.579500 number of atom coordinates read : 3038 total number of charged atoms : 2886 net assigned charge : -5.687977 assigned positive charge : 447.2592 centred at (gu) : 91.49682 93.52740 86.14410 assigned negative charge : -452.9486 centred at (gu) : 91.58505 93.93253 85.99206 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 88682 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26145 grid for indexing accessible points = 1.400000 m= 32402 mr = 62094 m= 5554 mr = 23756 m= 324 mr = 3561 m= 4 mr = 114 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 37441 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 140 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 22720 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) : 0.6361119 object centre at (A) : 10.93000 29.92650 -6.579500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0162646E-02 2.5045566E-02 midg,1,midg; midg,igrid,midg -1.9648053E-02 -4.4835787E-02 1,midg,midg; igrid,midg,midg -1.6845526E-02 -3.8658388E-02 gauss-seidel spectral radius is 0.9986787 estimated iterations to convergence 218 setup time was (sec) 0.8500000 now iterating at: 16:00:29 rms-change max change #iterations 4.641135 192.4595 at 10iterations 2.199552 70.45639 at 20iterations 1.041290 31.06982 at 30iterations 0.4943021 14.99888 at 40iterations 0.2341625 6.762863 at 50iterations 0.1113752 3.239708 at 60iterations 5.2733254E-02 1.613117 at 70iterations 2.4996955E-02 0.7261772 at 80iterations 1.1895087E-02 0.3138943 at 90iterations 5.6763231E-03 0.1632423 at 100iterations 2.7477415E-03 7.7938080E-02 at 110iterations 1.3517009E-03 4.2644501E-02 at 120iterations finished qdiffx linear iterations at : 16:00:35 total time elapsed so far: 6.860000 # loops : 120 mean,max change (kT/e) : 1.3517009E-03 4.2644501E-02 energy calculations done at 6.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.060000 DelPhi exited at 16:00:35 7.060u 0.169s 0:07.49 96.3% 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 Sun Oct 9 2011 at 16:00:35 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3038 !!! WARNING: GLM 156 has a net charge of -0.0940 !!! WARNING: GLM 225 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.862503 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): -15.20100 37.06100 ymin,ymax (A): 3.634000 56.21900 zmin,zma (A): -34.56200 21.40300 x,y,z range (A): 52.26200 52.58500 55.96500 scale (grids/A): 2.862503 object centre (A): 10.93000 29.92650 -6.579500 number of atom coordinates read : 3038 total number of charged atoms : 2886 net assigned charge : -5.687977 assigned positive charge : 447.2592 centred at (gu) : 92.24495 95.29108 84.21602 assigned negative charge : -452.9486 centred at (gu) : 92.37746 95.89876 83.98796 start vw surface at 0.1500000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 205416 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26145 grid for indexing accessible points = 1.400000 m= 104051 mr = 150577 m= 38881 mr = 84974 m= 10040 mr = 31197 m= 1451 mr = 7548 m= 65 mr = 968 m= 0 mr = 25 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.520000 number of dielectric boundary points 84615 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.630000 number of grid points assigned charge 23087 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) : 1.908336 object centre at (A) : 10.93000 29.92650 -6.579500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2049347 0.6887934 midg,1,midg; midg,igrid,midg -0.3349802 -0.4454150 1,midg,midg; igrid,midg,midg -0.2703811 -0.3991852 gauss-seidel spectral radius is 0.9992805 estimated iterations to convergence 294 setup time was (sec) 1.790000 now iterating at: 16:00:37 rms-change max change #iterations 10.91363 374.2994 at 10iterations 6.465317 127.2004 at 20iterations 3.789984 69.60153 at 30iterations 2.222754 43.02295 at 40iterations 1.300571 26.94287 at 50iterations 0.7611451 15.28891 at 60iterations 0.4429082 8.003033 at 70iterations 0.2579589 4.888336 at 80iterations 0.1500893 2.612803 at 90iterations 8.7186269E-02 1.514370 at 100iterations 5.0692454E-02 0.9253836 at 110iterations 2.9502546E-02 0.4901352 at 120iterations 1.7133579E-02 0.2917938 at 130iterations 1.0005665E-02 0.1958189 at 140iterations 5.8656815E-03 0.1096067 at 150iterations 3.4705850E-03 7.6246262E-02 at 160iterations 2.1077299E-03 4.1512489E-02 at 170iterations 1.3223396E-03 2.9153824E-02 at 180iterations finished qdiffx linear iterations at : 16:00:47 total time elapsed so far: 11.28000 # loops : 180 mean,max change (kT/e) : 1.3223396E-03 2.9153824E-02 energy calculations done at 11.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.45000 DelPhi exited at 16:00:47 11.452u 0.176s 0:11.96 97.1% 0+0k 0+0io 0pf+0w