Sun Oct 9 14:38:12 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 Sun Oct 9 2011 at 14:38:12 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 = 1413 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7871404 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): 8.186000 42.28400 ymin,ymax (A): 23.26900 63.22400 zmin,zma (A): -9.591001 35.63600 x,y,z range (A): 34.09800 39.95500 45.22700 scale (grids/A): 0.7871404 object centre (A): 25.23500 43.24650 13.02250 number of atom coordinates read : 1413 total number of charged atoms : 1282 net assigned charge : 2.9504299E-06 assigned positive charge : 208.5353 centred at (gu) : 89.65802 91.09021 91.64535 assigned negative charge : -208.5351 centred at (gu) : 89.61913 90.98997 91.39925 start vw surface at 5.9999999E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 5907 nv = 96 ne = 84 npr = 30621 no. pairs analyzed = 30621 no. exposed pairs = 1711 no. arc points = 12492 no. surface atoms = 575 nbur = 838 mkacc time = 4.9999997E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 450 mr = 3316 m= 5 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 5.9999995E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1300000 number of dielectric boundary points 2965 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 957 ## 73 charges are in solution ## iepsmp to db, and charging done at 0.1900000 number of grid points assigned charge 5941 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.1135417E-07 5.1933296E-07 midg,1,midg; midg,igrid,midg -1.4242359E-07 1.8737013E-07 1,midg,midg; igrid,midg,midg -7.6780310E-08 5.1390852E-08 gauss-seidel spectral radius is 0.9915050 estimated iterations to convergence 88 setup time was (sec) 0.3100000 now iterating at: 14:38:12 rms-change max change #iterations 0.2521864 40.60709 at 10iterations 3.8181446E-02 6.471992 at 20iterations 5.6432588E-03 0.8167810 at 30iterations 8.4543321E-04 0.1267853 at 40iterations 1.2958169E-04 1.9203186E-02 at 50iterations finished qdiffx linear iterations at : 14:38:15 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 1.2958169E-04 1.9203186E-02 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 14:38:15 3.354u 0.196s 0:03.87 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 Sun Oct 9 2011 at 14:38:16 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 = 1413 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.361421 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): 8.186000 42.28400 ymin,ymax (A): 23.26900 63.22400 zmin,zma (A): -9.591001 35.63600 x,y,z range (A): 34.09800 39.95500 45.22700 scale (grids/A): 2.361421 object centre (A): 25.23500 43.24650 13.02250 number of atom coordinates read : 1413 total number of charged atoms : 1282 net assigned charge : 2.9504299E-06 assigned positive charge : 208.5353 centred at (gu) : 88.97403 93.27100 94.93630 assigned negative charge : -208.5351 centred at (gu) : 88.85753 92.96998 94.19794 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 61535 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12492 grid for indexing accessible points = 1.400000 m= 24788 mr = 42421 m= 5470 mr = 18996 m= 734 mr = 3689 m= 53 mr = 428 m= 0 mr = 20 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 27026 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 10232 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) : 0.7871404 object centre at (A) : 25.23500 43.24650 13.02250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9948211E-02 8.0488563E-02 midg,1,midg; midg,igrid,midg -3.7156813E-02 1.7674502E-02 1,midg,midg; igrid,midg,midg 1.2684438E-03 -9.2233364E-03 gauss-seidel spectral radius is 0.9989603 estimated iterations to convergence 245 setup time was (sec) 0.5600000 now iterating at: 14:38:16 rms-change max change #iterations 4.486734 252.1610 at 10iterations 2.303000 94.37531 at 20iterations 1.186586 37.85316 at 30iterations 0.6149285 19.76693 at 40iterations 0.3167689 10.20299 at 50iterations 0.1636875 4.923721 at 60iterations 8.4603541E-02 2.790866 at 70iterations 4.3573268E-02 1.437008 at 80iterations 2.2468612E-02 0.7322164 at 90iterations 1.1583240E-02 0.3804665 at 100iterations 5.9987456E-03 0.1920090 at 110iterations 3.0802465E-03 9.6557617E-02 at 120iterations finished qdiffx linear iterations at : 14:38:23 total time elapsed so far: 7.690000 # loops : 120 mean,max change (kT/e) : 3.0802465E-03 9.6557617E-02 energy calculations done at 7.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.840000 DelPhi exited at 14:38:24 7.842u 0.177s 0:08.36 95.8% 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 14:38:24 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1413 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.542132 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): 8.186000 42.28400 ymin,ymax (A): 23.26900 63.22400 zmin,zma (A): -9.591001 35.63600 x,y,z range (A): 34.09800 39.95500 45.22700 scale (grids/A): 3.542132 object centre (A): 25.23500 43.24650 13.02250 number of atom coordinates read : 1413 total number of charged atoms : 1282 net assigned charge : 2.9504299E-06 assigned positive charge : 208.5353 centred at (gu) : 88.46111 94.90658 97.40441 assigned negative charge : -208.5351 centred at (gu) : 88.28630 94.45500 96.29694 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 141525 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12492 grid for indexing accessible points = 1.400000 m= 75221 mr = 101765 m= 32883 mr = 62772 m= 10651 mr = 27472 m= 2815 mr = 8259 m= 541 mr = 2069 m= 76 mr = 388 m= 1 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.020000 number of dielectric boundary points 60943 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 10256 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) : 2.361421 object centre at (A) : 25.23500 43.24650 13.02250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.4378088E-02 0.5621454 midg,1,midg; midg,igrid,midg -0.3131068 0.1782047 1,midg,midg; igrid,midg,midg 3.7628613E-02 -0.1077794 gauss-seidel spectral radius is 0.9993142 estimated iterations to convergence 301 setup time was (sec) 1.240000 now iterating at: 14:38:25 rms-change max change #iterations 9.461086 368.3617 at 10iterations 5.568078 139.3206 at 20iterations 3.263792 68.53600 at 30iterations 1.912624 34.17156 at 40iterations 1.120351 22.28616 at 50iterations 0.6569397 12.49597 at 60iterations 0.3838645 7.039968 at 70iterations 0.2248081 4.107918 at 80iterations 0.1317454 2.473174 at 90iterations 7.7204861E-02 1.329884 at 100iterations 4.5179147E-02 0.7837791 at 110iterations 2.6515389E-02 0.4738531 at 120iterations 1.5532892E-02 0.2847505 at 130iterations 9.1134068E-03 0.1532526 at 140iterations 5.3370153E-03 9.9052429E-02 at 150iterations 3.1289479E-03 5.9795380E-02 at 160iterations 1.8319458E-03 3.2730103E-02 at 170iterations 1.0766924E-03 1.9481659E-02 at 180iterations finished qdiffx linear iterations at : 14:38:37 total time elapsed so far: 12.45000 # loops : 180 mean,max change (kT/e) : 1.0766924E-03 1.9481659E-02 energy calculations done at 12.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.60000 DelPhi exited at 14:38:37 12.599u 0.208s 0:13.10 97.6% 0+0k 0+0io 0pf+0w