Mon Oct 10 19:35:33 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 Mon Oct 10 2011 at 19:35:34 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2493 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: 0.5879341 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): 8.042001 56.23200 ymin,ymax (A): -28.32100 24.11400 zmin,zma (A): 2.416000 62.96700 x,y,z range (A): 48.19000 52.43500 60.55100 scale (grids/A): 0.5879341 object centre (A): 32.13700 -2.103500 32.69150 number of atom coordinates read : 2493 total number of charged atoms : 2359 net assigned charge : 3.000018 assigned positive charge : 363.3520 centred at (gu) : 92.44436 90.33739 89.45856 assigned negative charge : -360.3530 centred at (gu) : 92.49911 90.30986 89.43586 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5922 nv = 96 ne = 84 npr = 48712 no. pairs analyzed = 48712 no. exposed pairs = 3557 no. arc points = 25402 no. surface atoms = 1189 nbur = 1304 mkacc time = 0.1400000 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 = 1.456000 m= 304 mr = 2807 m= 1 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3388 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2578 ## 303 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7323 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.1165846E-10 1.2462742E-09 midg,1,midg; midg,igrid,midg 2.3976926E-10 1.6421263E-09 1,midg,midg; igrid,midg,midg 1.2269317E-09 -7.1787121E-10 gauss-seidel spectral radius is 0.9850420 estimated iterations to convergence 67 setup time was (sec) 0.6200000 now iterating at: 19:35:34 rms-change max change #iterations 9.2906207E-02 19.51331 at 10iterations 7.5854994E-03 1.318581 at 20iterations 7.4688188E-04 0.1119423 at 30iterations 1.0927327E-04 1.8474579E-02 at 40iterations 2.2345672E-05 3.8833618E-03 at 50iterations finished qdiffx linear iterations at : 19:35:38 total time elapsed so far: 3.960000 # loops : 50 mean,max change (kT/e) : 2.2345672E-05 3.8833618E-03 energy calculations done at 3.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.140000 DelPhi exited at 19:35:39 4.146u 0.260s 0:05.08 86.6% 0+0k 0+0io 6pf+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 19:35:39 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2493 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: 1.763802 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): 8.042001 56.23200 ymin,ymax (A): -28.32100 24.11400 zmin,zma (A): 2.416000 62.96700 x,y,z range (A): 48.19000 52.43500 60.55100 scale (grids/A): 1.763802 object centre (A): 32.13700 -2.103500 32.69150 number of atom coordinates read : 2493 total number of charged atoms : 2359 net assigned charge : 3.000018 assigned positive charge : 363.3520 centred at (gu) : 97.33273 91.01167 88.37515 assigned negative charge : -360.3530 centred at (gu) : 97.49745 90.92964 88.30754 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 64403 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25402 grid for indexing accessible points = 1.400000 m= 20573 mr = 41203 m= 2821 mr = 13924 m= 115 mr = 1481 m= 3 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 31291 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 231 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 18408 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) : 0.5879341 object centre at (A) : 32.13700 -2.103500 32.69150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2135993E-02 1.1470722E-02 midg,1,midg; midg,igrid,midg 2.5322011E-03 2.8258674E-03 1,midg,midg; igrid,midg,midg 1.1375855E-02 4.4477829E-03 gauss-seidel spectral radius is 0.9984269 estimated iterations to convergence 200 setup time was (sec) 0.8800000 now iterating at: 19:35:40 rms-change max change #iterations 3.493206 177.3168 at 10iterations 1.529006 57.11382 at 20iterations 0.6740428 22.72080 at 30iterations 0.2979416 10.76354 at 40iterations 0.1315979 4.809475 at 50iterations 5.8139198E-02 2.134109 at 60iterations 2.5710253E-02 0.9824657 at 70iterations 1.1415413E-02 0.4120874 at 80iterations 5.0776685E-03 0.1816673 at 90iterations 2.2733335E-03 7.8215599E-02 at 100iterations 1.0288263E-03 3.9606094E-02 at 110iterations 4.7595106E-04 2.0195007E-02 at 120iterations finished qdiffx linear iterations at : 19:35:48 total time elapsed so far: 9.300000 # loops : 120 mean,max change (kT/e) : 4.7595106E-04 2.0195007E-02 energy calculations done at 9.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.480000 DelPhi exited at 19:35:49 9.484u 0.323s 0:10.18 96.2% 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 Mon Oct 10 2011 at 19:35:49 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2493 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: 2.645704 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): 8.042001 56.23200 ymin,ymax (A): -28.32100 24.11400 zmin,zma (A): 2.416000 62.96700 x,y,z range (A): 48.19000 52.43500 60.55100 scale (grids/A): 2.645704 object centre (A): 32.13700 -2.103500 32.69150 number of atom coordinates read : 2493 total number of charged atoms : 2359 net assigned charge : 3.000018 assigned positive charge : 363.3520 centred at (gu) : 100.9988 91.51740 87.56260 assigned negative charge : -360.3530 centred at (gu) : 101.2461 91.39448 87.46120 start vw surface at 0.1600000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 148850 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25402 grid for indexing accessible points = 1.400000 m= 68551 mr = 100966 m= 22263 mr = 53286 m= 4631 mr = 16545 m= 457 mr = 3199 m= 11 mr = 228 m= 0 mr = 0 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.430000 number of dielectric boundary points 70539 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.580000 number of grid points assigned charge 18864 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) : 1.763802 object centre at (A) : 32.13700 -2.103500 32.69150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3643721 0.2429664 midg,1,midg; midg,igrid,midg 8.7286476E-03 1.3107568E-03 1,midg,midg; igrid,midg,midg 0.1509703 -4.1183516E-02 gauss-seidel spectral radius is 0.9992129 estimated iterations to convergence 281 setup time was (sec) 1.750000 now iterating at: 19:35:51 rms-change max change #iterations 8.818727 258.9634 at 10iterations 5.165826 121.6479 at 20iterations 2.981864 82.54533 at 30iterations 1.711275 34.94268 at 40iterations 0.9780809 21.61615 at 50iterations 0.5575598 12.47558 at 60iterations 0.3172629 6.089184 at 70iterations 0.1796498 3.725533 at 80iterations 0.1018776 2.180550 at 90iterations 5.7720222E-02 1.132435 at 100iterations 3.2731999E-02 0.6693635 at 110iterations 1.8529989E-02 0.4378140 at 120iterations 1.0506487E-02 0.2105217 at 130iterations 5.9633916E-03 0.1398888 at 140iterations 3.4181783E-03 7.1004391E-02 at 150iterations 1.9746029E-03 4.6453476E-02 at 160iterations 1.1562498E-03 2.6706696E-02 at 170iterations 6.9147360E-04 1.5071869E-02 at 180iterations finished qdiffx linear iterations at : 19:36:05 total time elapsed so far: 15.66000 # loops : 180 mean,max change (kT/e) : 6.9147360E-04 1.5071869E-02 energy calculations done at 15.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.85000 DelPhi exited at 19:36:05 15.849u 0.334s 0:16.47 98.1% 0+0k 0+0io 0pf+0w