Sat Oct 8 11:39:17 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 11:39:17 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3350 !!! WARNING: HIZ 15 has a net charge of 0.2000 !!! WARNING: HIZ 17 has a net charge of 0.2000 !!! WARNING: HIZ 214 has a net charge of 0.2000 !!! WARNING: HIR 238 has a net charge of 0.5140 !!! WARNING: ZN4 466 has a net charge of 1.4000 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: 0.6456410 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): -23.39800 31.74100 ymin,ymax (A): -1.784000 50.85300 zmin,zma (A): 11.92900 59.91600 x,y,z range (A): 55.13900 52.63700 47.98700 scale (grids/A): 0.6456410 object centre (A): 4.171500 24.53450 35.92250 number of atom coordinates read : 3350 total number of charged atoms : 3224 net assigned charge : -0.9859697 assigned positive charge : 514.1633 centred at (gu) : 91.04543 90.87961 89.22101 assigned negative charge : -515.1504 centred at (gu) : 91.11648 90.68715 89.38129 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 9185 nv = 96 ne = 84 npr = 70233 no. pairs analyzed = 70233 no. exposed pairs = 3672 no. arc points = 24858 no. surface atoms = 1268 nbur = 2082 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 498 mr = 5639 m= 3 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3980 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2477 ## 222 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 11205 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.1165623E-08 -2.6567227E-08 midg,1,midg; midg,igrid,midg -3.0977890E-08 3.8610729E-08 1,midg,midg; igrid,midg,midg 8.4722203E-09 -1.8747258E-08 gauss-seidel spectral radius is 0.9876214 estimated iterations to convergence 73 setup time was (sec) 0.4800000 now iterating at: 11:39:18 rms-change max change #iterations 0.1848770 25.05746 at 10iterations 1.8712964E-02 2.385440 at 20iterations 1.9363180E-03 0.2421417 at 30iterations 2.0079577E-04 2.5863647E-02 at 40iterations 2.4171271E-05 3.1585693E-03 at 50iterations finished qdiffx linear iterations at : 11:39:21 total time elapsed so far: 3.930000 # loops : 50 mean,max change (kT/e) : 2.4171271E-05 3.1585693E-03 energy calculations done at 3.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.060000 DelPhi exited at 11:39:22 4.067u 0.262s 0:04.63 93.3% 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 11:39:22 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3350 !!! WARNING: HIZ 15 has a net charge of 0.2000 !!! WARNING: HIZ 17 has a net charge of 0.2000 !!! WARNING: HIZ 214 has a net charge of 0.2000 !!! WARNING: HIR 238 has a net charge of 0.5140 !!! WARNING: ZN4 466 has a net charge of 1.4000 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: 1.936923 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): -23.39800 31.74100 ymin,ymax (A): -1.784000 50.85300 zmin,zma (A): 11.92900 59.91600 x,y,z range (A): 55.13900 52.63700 47.98700 scale (grids/A): 1.936923 object centre (A): 4.171500 24.53450 35.92250 number of atom coordinates read : 3350 total number of charged atoms : 3224 net assigned charge : -0.9859697 assigned positive charge : 514.1633 centred at (gu) : 93.13569 92.63790 87.66245 assigned negative charge : -515.1504 centred at (gu) : 93.34878 92.06100 88.14342 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 99281 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24858 grid for indexing accessible points = 1.400000 m= 39233 mr = 73291 m= 6439 mr = 30908 m= 364 mr = 4361 m= 2 mr = 160 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 77 time to turn everything in is 0.5000000 number of dielectric boundary points 36599 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 156 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 25410 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) : 0.6456410 object centre at (A) : 4.171500 24.53450 35.92250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0113463E-02 -5.9946634E-02 midg,1,midg; midg,igrid,midg -3.9565284E-02 4.6991155E-02 1,midg,midg; igrid,midg,midg 9.6205408E-03 -1.5838405E-02 gauss-seidel spectral radius is 0.9987313 estimated iterations to convergence 222 setup time was (sec) 0.7800000 now iterating at: 11:39:23 rms-change max change #iterations 5.152999 168.2830 at 10iterations 2.485977 74.67355 at 20iterations 1.195652 32.34605 at 30iterations 0.5774168 15.43003 at 40iterations 0.2781796 8.969044 at 50iterations 0.1340810 3.631584 at 60iterations 6.4790741E-02 1.757736 at 70iterations 3.1259671E-02 0.9156253 at 80iterations 1.5100009E-02 0.4133244 at 90iterations 7.2684488E-03 0.2322998 at 100iterations 3.4976397E-03 9.1917038E-02 at 110iterations 1.6984597E-03 4.5166016E-02 at 120iterations finished qdiffx linear iterations at : 11:39:32 total time elapsed so far: 9.350000 # loops : 120 mean,max change (kT/e) : 1.6984597E-03 4.5166016E-02 energy calculations done at 9.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.480000 DelPhi exited at 11:39:33 9.486u 0.303s 0:10.70 91.4% 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 11:39:33 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3350 !!! WARNING: HIZ 15 has a net charge of 0.2000 !!! WARNING: HIZ 17 has a net charge of 0.2000 !!! WARNING: HIZ 214 has a net charge of 0.2000 !!! WARNING: HIR 238 has a net charge of 0.5140 !!! WARNING: ZN4 466 has a net charge of 1.4000 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: 2.905385 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): -23.39800 31.74100 ymin,ymax (A): -1.784000 50.85300 zmin,zma (A): 11.92900 59.91600 x,y,z range (A): 55.13900 52.63700 47.98700 scale (grids/A): 2.905385 object centre (A): 4.171500 24.53450 35.92250 number of atom coordinates read : 3350 total number of charged atoms : 3224 net assigned charge : -0.9859697 assigned positive charge : 514.1633 centred at (gu) : 94.70332 93.95663 86.49355 assigned negative charge : -515.1504 centred at (gu) : 95.02303 93.09151 87.21495 start vw surface at 0.1000000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 229688 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24858 grid for indexing accessible points = 1.400000 m= 124771 mr = 176157 m= 48475 mr = 106146 m= 11793 mr = 41132 m= 1705 mr = 9360 m= 111 mr = 1160 m= 1 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 227 time to turn everything in is 1.390000 number of dielectric boundary points 82539 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 25792 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) : 1.936923 object centre at (A) : 4.171500 24.53450 35.92250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1161969 -0.7354388 midg,1,midg; midg,igrid,midg -0.3492891 0.4824293 1,midg,midg; igrid,midg,midg -3.1326909E-02 -7.8611158E-02 gauss-seidel spectral radius is 0.9992866 estimated iterations to convergence 295 setup time was (sec) 1.690000 now iterating at: 11:39:35 rms-change max change #iterations 11.83149 407.7318 at 10iterations 6.973085 154.0078 at 20iterations 4.097663 74.55283 at 30iterations 2.400212 38.20595 at 40iterations 1.399643 25.06884 at 50iterations 0.8168991 14.04843 at 60iterations 0.4760820 6.925606 at 70iterations 0.2771430 4.471222 at 80iterations 0.1614517 2.661360 at 90iterations 9.4024032E-02 1.412815 at 100iterations 5.4706257E-02 0.8685265 at 110iterations 3.1770926E-02 0.5013156 at 120iterations 1.8505182E-02 0.2788916 at 130iterations 1.0754040E-02 0.1675262 at 140iterations 6.2608426E-03 0.1012640 at 150iterations 3.6485216E-03 5.7914734E-02 at 160iterations 2.1300847E-03 3.1776428E-02 at 170iterations 1.2423252E-03 2.0876408E-02 at 180iterations finished qdiffx linear iterations at : 11:39:49 total time elapsed so far: 16.34000 # loops : 180 mean,max change (kT/e) : 1.2423252E-03 2.0876408E-02 energy calculations done at 16.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.47000 DelPhi exited at 11:39:50 16.469u 0.330s 0:17.11 98.1% 0+0k 0+0io 0pf+0w