Mon Oct 10 18:36:03 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 18:36:03 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 = 2236 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6896685 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): 28.39100 73.73900 ymin,ymax (A): 16.05100 65.73600 zmin,zma (A): 4.919000 56.53800 x,y,z range (A): 45.34800 49.68500 51.61900 scale (grids/A): 0.6896685 object centre (A): 51.06500 40.89350 30.72850 number of atom coordinates read : 2236 total number of charged atoms : 2100 net assigned charge : 2.500006 assigned positive charge : 331.0102 centred at (gu) : 89.46310 88.24278 88.73709 assigned negative charge : -328.5107 centred at (gu) : 89.43388 88.39996 88.65221 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7006 nv = 96 ne = 84 npr = 46041 no. pairs analyzed = 46041 no. exposed pairs = 2784 no. arc points = 19508 no. surface atoms = 940 nbur = 1296 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 457 mr = 3779 m= 2 mr = 93 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 130 time to turn everything in is 0.1800000 number of dielectric boundary points 3593 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1740 ## 143 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8106 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.1583128E-08 3.2787593E-08 midg,1,midg; midg,igrid,midg 9.5132947E-08 -2.9237826E-08 1,midg,midg; igrid,midg,midg 3.2496663E-09 2.0842345E-08 gauss-seidel spectral radius is 0.9890655 estimated iterations to convergence 78 setup time was (sec) 0.3700000 now iterating at: 18:36:03 rms-change max change #iterations 0.1859864 26.19460 at 10iterations 2.1750005E-02 3.417165 at 20iterations 2.5358424E-03 0.3266649 at 30iterations 2.9911465E-04 3.9000511E-02 at 40iterations 3.5166689E-05 4.7988892E-03 at 50iterations finished qdiffx linear iterations at : 18:36:06 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 3.5166689E-05 4.7988892E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 18:36:07 3.441u 0.161s 0:03.94 91.3% 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 Mon Oct 10 2011 at 18:36:07 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 = 2236 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.069005 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): 28.39100 73.73900 ymin,ymax (A): 16.05100 65.73600 zmin,zma (A): 4.919000 56.53800 x,y,z range (A): 45.34800 49.68500 51.61900 scale (grids/A): 2.069005 object centre (A): 51.06500 40.89350 30.72850 number of atom coordinates read : 2236 total number of charged atoms : 2100 net assigned charge : 2.500006 assigned positive charge : 331.0102 centred at (gu) : 88.38878 84.72768 86.21086 assigned negative charge : -328.5107 centred at (gu) : 88.30167 85.19952 85.95646 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 74665 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19508 grid for indexing accessible points = 1.400000 m= 27828 mr = 50966 m= 5329 mr = 20616 m= 426 mr = 3482 m= 13 mr = 213 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 3456 time to turn everything in is 0.3800000 number of dielectric boundary points 32982 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 86 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 16673 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) : 0.6896685 object centre at (A) : 51.06500 40.89350 30.72850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1031593E-02 4.8347689E-02 midg,1,midg; midg,igrid,midg 4.6812624E-02 -2.1298399E-02 1,midg,midg; igrid,midg,midg 1.4978886E-02 1.5244661E-02 gauss-seidel spectral radius is 0.9987966 estimated iterations to convergence 228 setup time was (sec) 0.6000000 now iterating at: 18:36:08 rms-change max change #iterations 4.530090 220.7164 at 10iterations 2.211043 74.74902 at 20iterations 1.081793 34.13971 at 30iterations 0.5317703 15.81590 at 40iterations 0.2609554 8.025751 at 50iterations 0.1278226 3.859063 at 60iterations 6.2745921E-02 1.843117 at 70iterations 3.0633101E-02 1.010345 at 80iterations 1.5039803E-02 0.4373016 at 90iterations 7.3834588E-03 0.2209396 at 100iterations 3.6125723E-03 0.1131973 at 110iterations 1.7774444E-03 5.5078626E-02 at 120iterations finished qdiffx linear iterations at : 18:36:15 total time elapsed so far: 7.810000 # loops : 120 mean,max change (kT/e) : 1.7774444E-03 5.5078626E-02 energy calculations done at 7.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.950000 DelPhi exited at 18:36:16 7.952u 0.195s 0:08.65 94.1% 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 18:36:16 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 = 2236 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.103508 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): 28.39100 73.73900 ymin,ymax (A): 16.05100 65.73600 zmin,zma (A): 4.919000 56.53800 x,y,z range (A): 45.34800 49.68500 51.61900 scale (grids/A): 3.103508 object centre (A): 51.06500 40.89350 30.72850 number of atom coordinates read : 2236 total number of charged atoms : 2100 net assigned charge : 2.500006 assigned positive charge : 331.0102 centred at (gu) : 87.58302 82.09130 84.31620 assigned negative charge : -328.5107 centred at (gu) : 87.45241 82.79922 83.93449 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 172482 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19508 grid for indexing accessible points = 1.400000 m= 87330 mr = 123776 m= 35095 mr = 71016 m= 9815 mr = 28577 m= 1722 mr = 7632 m= 167 mr = 1243 m= 12 mr = 91 m= 0 mr = 0 time to grow re-entrant surface = 0.5600000 no. cavity mid-points inaccessible to solvent = 11817 time to turn everything in is 1.150000 number of dielectric boundary points 74288 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.240000 number of grid points assigned charge 16796 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) : 2.069005 object centre at (A) : 51.06500 40.89350 30.72850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8335208E-04 0.9121903 midg,1,midg; midg,igrid,midg 0.4141319 -0.1237443 1,midg,midg; igrid,midg,midg 0.2013039 4.6181824E-02 gauss-seidel spectral radius is 0.9992940 estimated iterations to convergence 297 setup time was (sec) 1.390000 now iterating at: 18:36:17 rms-change max change #iterations 10.31694 379.2604 at 10iterations 6.089412 133.3889 at 20iterations 3.588559 78.80039 at 30iterations 2.102364 56.04205 at 40iterations 1.230041 22.80238 at 50iterations 0.7212874 14.06223 at 60iterations 0.4206892 7.895473 at 70iterations 0.2454772 4.280792 at 80iterations 0.1429628 2.571678 at 90iterations 8.3528042E-02 1.534788 at 100iterations 4.8613824E-02 0.8104477 at 110iterations 2.8315417E-02 0.5550919 at 120iterations 1.6515741E-02 0.2714653 at 130iterations 9.6192369E-03 0.1679192 at 140iterations 5.6010494E-03 9.0995312E-02 at 150iterations 3.2672428E-03 5.6269407E-02 at 160iterations 1.9024888E-03 3.2115936E-02 at 170iterations 1.1124937E-03 1.9537926E-02 at 180iterations finished qdiffx linear iterations at : 18:36:29 total time elapsed so far: 12.84000 # loops : 180 mean,max change (kT/e) : 1.1124937E-03 1.9537926E-02 energy calculations done at 12.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.97000 DelPhi exited at 18:36:29 12.975u 0.207s 0:13.56 97.1% 0+0k 0+0io 0pf+0w