Sat Oct 15 15:29:15 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+sph.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 = amb.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 15:29:15 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2737 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: 0.6408756 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): -12.47200 36.76600 ymin,ymax (A): -25.97200 22.32300 zmin,zma (A): -10.13500 45.41400 x,y,z range (A): 49.23800 48.29500 55.54900 scale (grids/A): 0.6408756 object centre (A): 12.14700 -1.824500 17.63950 number of atom coordinates read : 2737 total number of charged atoms : 2588 net assigned charge : 1.500015 assigned positive charge : 414.4257 centred at (gu) : 90.52509 90.43600 91.84325 assigned negative charge : -412.9263 centred at (gu) : 90.29310 90.28327 91.75682 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7415 nv = 96 ne = 84 npr = 56116 no. pairs analyzed = 56116 no. exposed pairs = 3311 no. arc points = 23054 no. surface atoms = 1126 nbur = 1611 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 359 mr = 4135 m= 4 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3603 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2345 ## 255 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9056 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.1881327E-09 1.8907125E-08 midg,1,midg; midg,igrid,midg -1.6250812E-08 2.2893788E-08 1,midg,midg; igrid,midg,midg -2.5278233E-08 3.4141753E-08 gauss-seidel spectral radius is 0.9873935 estimated iterations to convergence 73 setup time was (sec) 0.6100000 now iterating at: 15:29:17 rms-change max change #iterations 0.1500275 22.33833 at 10iterations 1.5015026E-02 2.148487 at 20iterations 1.5675912E-03 0.2173882 at 30iterations 1.7350490E-04 2.6784420E-02 at 40iterations 2.4706973E-05 3.1814575E-03 at 50iterations finished qdiffx linear iterations at : 15:29:20 total time elapsed so far: 3.900000 # loops : 50 mean,max change (kT/e) : 2.4706973E-05 3.1814575E-03 energy calculations done at 3.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.070000 DelPhi exited at 15:29:21 4.074u 0.404s 0:05.41 82.6% 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 Sat Oct 15 2011 at 15:29:21 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2737 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: 1.922627 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): -12.47200 36.76600 ymin,ymax (A): -25.97200 22.32300 zmin,zma (A): -10.13500 45.41400 x,y,z range (A): 49.23800 48.29500 55.54900 scale (grids/A): 1.922627 object centre (A): 12.14700 -1.824500 17.63950 number of atom coordinates read : 2737 total number of charged atoms : 2588 net assigned charge : 1.500015 assigned positive charge : 414.4257 centred at (gu) : 91.57468 91.30736 95.52890 assigned negative charge : -412.9263 centred at (gu) : 90.87914 90.84953 95.27039 start vw surface at 0.1200000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 80347 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23054 grid for indexing accessible points = 1.400000 m= 28944 mr = 56611 m= 4395 mr = 21378 m= 224 mr = 2666 m= 1 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 199 time to turn everything in is 0.6300000 number of dielectric boundary points 33180 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 173 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 20378 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) : 0.6408756 object centre at (A) : 12.14700 -1.824500 17.63950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.8495118E-02 9.5531801E-03 midg,1,midg; midg,igrid,midg -1.3471368E-02 1.2688726E-02 1,midg,midg; igrid,midg,midg -7.8918179E-03 6.2283464E-02 gauss-seidel spectral radius is 0.9986721 estimated iterations to convergence 217 setup time was (sec) 0.9200000 now iterating at: 15:29:22 rms-change max change #iterations 4.514067 187.7635 at 10iterations 2.134701 72.99207 at 20iterations 1.015475 31.68845 at 30iterations 0.4818183 15.81614 at 40iterations 0.2286681 6.954173 at 50iterations 0.1081189 3.419056 at 60iterations 5.1311169E-02 1.558784 at 70iterations 2.4297819E-02 0.7294691 at 80iterations 1.1538492E-02 0.3508892 at 90iterations 5.4741143E-03 0.1831493 at 100iterations 2.5981718E-03 8.4663391E-02 at 110iterations 1.2331220E-03 3.6534309E-02 at 120iterations finished qdiffx linear iterations at : 15:29:31 total time elapsed so far: 9.380000 # loops : 120 mean,max change (kT/e) : 1.2331220E-03 3.6534309E-02 energy calculations done at 9.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.550000 DelPhi exited at 15:29:31 9.559u 0.483s 0:10.68 93.9% 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 15:29:31 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2737 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: 2.883940 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): -12.47200 36.76600 ymin,ymax (A): -25.97200 22.32300 zmin,zma (A): -10.13500 45.41400 x,y,z range (A): 49.23800 48.29500 55.54900 scale (grids/A): 2.883940 object centre (A): 12.14700 -1.824500 17.63950 number of atom coordinates read : 2737 total number of charged atoms : 2588 net assigned charge : 1.500015 assigned positive charge : 414.4257 centred at (gu) : 92.36183 91.96096 98.29334 assigned negative charge : -412.9263 centred at (gu) : 91.31874 91.27433 97.90540 start vw surface at 0.1300000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 186001 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23054 grid for indexing accessible points = 1.400000 m= 94441 mr = 136935 m= 33281 mr = 77629 m= 7528 mr = 26678 m= 971 mr = 5545 m= 48 mr = 618 m= 0 mr = 20 time to grow re-entrant surface = 0.9900000 no. cavity mid-points inaccessible to solvent = 658 time to turn everything in is 1.670000 number of dielectric boundary points 74845 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.820000 number of grid points assigned charge 20704 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) : 1.922627 object centre at (A) : 12.14700 -1.824500 17.63950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7077327 0.3034584 midg,1,midg; midg,igrid,midg -0.1280771 0.1413659 1,midg,midg; igrid,midg,midg -2.4582572E-02 0.5901455 gauss-seidel spectral radius is 0.9992664 estimated iterations to convergence 291 setup time was (sec) 2.020000 now iterating at: 15:29:34 rms-change max change #iterations 10.43434 367.8341 at 10iterations 6.123529 122.5404 at 20iterations 3.572823 78.33241 at 30iterations 2.079760 38.83268 at 40iterations 1.206637 23.80913 at 50iterations 0.7005292 13.36137 at 60iterations 0.4052206 8.081244 at 70iterations 0.2346028 4.524272 at 80iterations 0.1361003 2.458633 at 90iterations 7.8647807E-02 1.426666 at 100iterations 4.5446280E-02 0.7695618 at 110iterations 2.6290353E-02 0.5086098 at 120iterations 1.5207200E-02 0.2638474 at 130iterations 8.7786214E-03 0.1441884 at 140iterations 5.1028039E-03 9.2834473E-02 at 150iterations 2.9802844E-03 5.5069327E-02 at 160iterations 1.7506548E-03 3.3323288E-02 at 170iterations 1.0384113E-03 1.9065857E-02 at 180iterations finished qdiffx linear iterations at : 15:29:49 total time elapsed so far: 16.93000 # loops : 180 mean,max change (kT/e) : 1.0384113E-03 1.9065857E-02 energy calculations done at 16.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.11000 DelPhi exited at 15:29:49 17.113u 0.485s 0:18.09 97.2% 0+0k 0+0io 0pf+0w