Sat Oct 8 11:50:00 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 8 2011 at 11:50:00 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3482 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: 0.5292028 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): -4.238000 49.53200 ymin,ymax (A): -22.36900 35.30400 zmin,zma (A): 18.79600 86.06700 x,y,z range (A): 53.77000 57.67300 67.27100 scale (grids/A): 0.5292028 object centre (A): 22.64700 6.467499 52.43150 number of atom coordinates read : 3482 total number of charged atoms : 3320 net assigned charge : -3.499992 assigned positive charge : 516.8338 centred at (gu) : 91.25906 91.65408 90.72649 assigned negative charge : -520.3356 centred at (gu) : 91.16241 91.62503 90.79684 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6270 nv = 96 ne = 84 npr = 68878 no. pairs analyzed = 68878 no. exposed pairs = 4609 no. arc points = 32553 no. surface atoms = 1556 nbur = 1926 mkacc time = 0.1800000 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 = 1.624000 m= 261 mr = 3106 m= 0 mr = 7 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 3418 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3298 ## 502 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 8442 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3777804E-10 -4.8533499E-10 midg,1,midg; midg,igrid,midg -1.5399484E-10 6.3879431E-12 1,midg,midg; igrid,midg,midg -3.7112430E-10 3.7898915E-10 gauss-seidel spectral radius is 0.9816470 estimated iterations to convergence 61 setup time was (sec) 0.6900000 now iterating at: 11:50:01 rms-change max change #iterations 6.9938883E-02 12.79686 at 10iterations 4.2407946E-03 0.6076088 at 20iterations 3.0906871E-04 4.3819427E-02 at 30iterations 5.0337010E-05 8.5210800E-03 at 40iterations 1.3580257E-05 2.3584366E-03 at 50iterations finished qdiffx linear iterations at : 11:50:05 total time elapsed so far: 4.880000 # loops : 50 mean,max change (kT/e) : 1.3580257E-05 2.3584366E-03 energy calculations done at 4.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.060000 DelPhi exited at 11:50:06 5.063u 0.378s 0:05.74 94.5% 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 Sat Oct 8 2011 at 11:50:06 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3482 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: 1.587608 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): -4.238000 49.53200 ymin,ymax (A): -22.36900 35.30400 zmin,zma (A): 18.79600 86.06700 x,y,z range (A): 53.77000 57.67300 67.27100 scale (grids/A): 1.587608 object centre (A): 22.64700 6.467499 52.43150 number of atom coordinates read : 3482 total number of charged atoms : 3320 net assigned charge : -3.499992 assigned positive charge : 516.8338 centred at (gu) : 93.77625 94.96078 92.17805 assigned negative charge : -520.3356 centred at (gu) : 93.48663 94.87477 92.38992 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 71031 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32553 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 20372 mr = 47182 m= 1884 mr = 13301 m= 55 mr = 849 m= 3 mr = 9 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 0.6000000 number of dielectric boundary points 32004 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 443 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 25203 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) : 0.5292028 object centre at (A) : 22.64700 6.467499 52.43150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3365942E-03 -7.4130362E-03 midg,1,midg; midg,igrid,midg 7.5247925E-05 3.9336635E-03 1,midg,midg; igrid,midg,midg -8.0736466E-03 -3.7263085E-03 gauss-seidel spectral radius is 0.9981259 estimated iterations to convergence 184 setup time was (sec) 0.9200000 now iterating at: 11:50:07 rms-change max change #iterations 3.399032 156.1776 at 10iterations 1.391584 55.36136 at 20iterations 0.5709188 22.90009 at 30iterations 0.2352421 8.065392 at 40iterations 9.6349165E-02 3.681013 at 50iterations 3.9697446E-02 1.478539 at 60iterations 1.6348593E-02 0.5813582 at 70iterations 6.7218537E-03 0.2235718 at 80iterations 2.7765315E-03 0.1023739 at 90iterations 1.1534070E-03 4.2098999E-02 at 100iterations 4.8060861E-04 1.6587257E-02 at 110iterations 2.0713796E-04 6.9093704E-03 at 120iterations finished qdiffx linear iterations at : 11:50:18 total time elapsed so far: 11.87000 # loops : 120 mean,max change (kT/e) : 2.0713796E-04 6.9093704E-03 energy calculations done at 11.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.04000 DelPhi exited at 11:50:19 12.042u 0.468s 0:12.84 97.3% 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 Sat Oct 8 2011 at 11:50:19 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3482 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: 2.381412 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): -4.238000 49.53200 ymin,ymax (A): -22.36900 35.30400 zmin,zma (A): 18.79600 86.06700 x,y,z range (A): 53.77000 57.67300 67.27100 scale (grids/A): 2.381412 object centre (A): 22.64700 6.467499 52.43150 number of atom coordinates read : 3482 total number of charged atoms : 3320 net assigned charge : -3.499992 assigned positive charge : 516.8338 centred at (gu) : 95.66418 97.44082 93.26682 assigned negative charge : -520.3356 centred at (gu) : 95.22990 97.31199 93.58475 start vw surface at 0.1400000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 165134 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32553 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 72104 mr = 116120 m= 18753 mr = 55478 m= 2794 mr = 13409 m= 178 mr = 1759 m= 0 mr = 62 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.430000 number of dielectric boundary points 72135 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 50 iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 26526 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) : 1.587608 object centre at (A) : 22.64700 6.467499 52.43150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1219549 -8.9216061E-02 midg,1,midg; midg,igrid,midg 8.4140506E-03 8.0888003E-02 1,midg,midg; igrid,midg,midg -8.6098231E-02 -8.8636473E-02 gauss-seidel spectral radius is 0.9991342 estimated iterations to convergence 268 setup time was (sec) 1.810000 now iterating at: 11:50:21 rms-change max change #iterations 9.060896 283.1789 at 10iterations 5.128724 134.0245 at 20iterations 2.878745 73.02235 at 30iterations 1.609089 41.59893 at 40iterations 0.8943507 20.87121 at 50iterations 0.4971865 11.37115 at 60iterations 0.2750375 5.887199 at 70iterations 0.1520013 3.366062 at 80iterations 8.3936691E-02 1.782305 at 90iterations 4.6294264E-02 0.9565344 at 100iterations 2.5543172E-02 0.5128081 at 110iterations 1.4077084E-02 0.2833317 at 120iterations 7.7441856E-03 0.1595173 at 130iterations 4.2626723E-03 8.6212158E-02 at 140iterations 2.3478088E-03 4.5527935E-02 at 150iterations 1.2934256E-03 2.4996758E-02 at 160iterations 7.1270944E-04 1.5499592E-02 at 170iterations 3.9473581E-04 8.2015991E-03 at 180iterations finished qdiffx linear iterations at : 11:50:39 total time elapsed so far: 19.87000 # loops : 180 mean,max change (kT/e) : 3.9473581E-04 8.2015991E-03 energy calculations done at 19.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.03000 DelPhi exited at 11:50:39 20.038u 0.515s 0:20.88 98.3% 0+0k 0+0io 0pf+0w