Tue Oct 11 07:33:16 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 Tue Oct 11 2011 at 07:33:16 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2569 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: 0.6613044 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): 18.20800 71.05500 ymin,ymax (A): -34.50600 15.97400 zmin,zma (A): 5.984000 59.81700 x,y,z range (A): 52.84700 50.48000 53.83300 scale (grids/A): 0.6613044 object centre (A): 44.63150 -9.266001 32.90050 number of atom coordinates read : 2569 total number of charged atoms : 2402 net assigned charge : -2.499994 assigned positive charge : 377.4972 centred at (gu) : 90.08823 87.24975 89.32044 assigned negative charge : -379.9977 centred at (gu) : 89.97686 87.17817 89.36837 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7701 nv = 96 ne = 84 npr = 52951 no. pairs analyzed = 52951 no. exposed pairs = 3051 no. arc points = 20728 no. surface atoms = 1051 nbur = 1518 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 460 mr = 4561 m= 4 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 48 time to turn everything in is 0.3700000 number of dielectric boundary points 3542 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2030 ## 159 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 8852 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.8758468E-09 -1.3665597E-08 midg,1,midg; midg,igrid,midg -3.6673971E-08 4.3578097E-09 1,midg,midg; igrid,midg,midg -2.8004923E-08 1.5984829E-08 gauss-seidel spectral radius is 0.9881446 estimated iterations to convergence 75 setup time was (sec) 0.6500000 now iterating at: 07:33:17 rms-change max change #iterations 0.1719803 22.42671 at 10iterations 1.8350320E-02 2.495073 at 20iterations 2.0391105E-03 0.3009033 at 30iterations 3.0362711E-04 3.9855003E-02 at 40iterations 7.0738701E-05 1.1177063E-02 at 50iterations finished qdiffx linear iterations at : 07:33:20 total time elapsed so far: 4.060000 # loops : 50 mean,max change (kT/e) : 7.0738701E-05 1.1177063E-02 energy calculations done at 4.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.240000 DelPhi exited at 07:33:21 4.247u 0.269s 0:04.99 90.1% 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 Tue Oct 11 2011 at 07:33:21 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2569 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: 1.983913 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): 18.20800 71.05500 ymin,ymax (A): -34.50600 15.97400 zmin,zma (A): 5.984000 59.81700 x,y,z range (A): 52.84700 50.48000 53.83300 scale (grids/A): 1.983913 object centre (A): 44.63150 -9.266001 32.90050 number of atom coordinates read : 2569 total number of charged atoms : 2402 net assigned charge : -2.499994 assigned positive charge : 377.4972 centred at (gu) : 90.26438 81.74868 87.96087 assigned negative charge : -379.9977 centred at (gu) : 89.93050 81.53432 88.10508 start vw surface at 0.1600000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 83148 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20728 grid for indexing accessible points = 1.400000 m= 33096 mr = 59988 m= 5788 mr = 25807 m= 361 mr = 3917 m= 2 mr = 161 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 1400 time to turn everything in is 0.7500000 number of dielectric boundary points 32523 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 120 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 18989 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) : 0.6613044 object centre at (A) : 44.63150 -9.266001 32.90050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.6254521E-03 5.0934742E-04 midg,1,midg; midg,igrid,midg 4.2198412E-02 2.2001483E-02 1,midg,midg; igrid,midg,midg -2.5779789E-02 -1.9956890E-02 gauss-seidel spectral radius is 0.9987276 estimated iterations to convergence 222 setup time was (sec) 1.060000 now iterating at: 07:33:22 rms-change max change #iterations 4.592792 179.1842 at 10iterations 2.216875 78.09303 at 20iterations 1.065408 35.21686 at 30iterations 0.5130461 15.37651 at 40iterations 0.2486363 8.080720 at 50iterations 0.1195777 3.529694 at 60iterations 5.7830166E-02 1.674235 at 70iterations 2.7949244E-02 0.8143502 at 80iterations 1.3453203E-02 0.4451103 at 90iterations 6.5196455E-03 0.1829948 at 100iterations 3.1804512E-03 0.1124687 at 110iterations 1.5569780E-03 4.7769547E-02 at 120iterations finished qdiffx linear iterations at : 07:33:31 total time elapsed so far: 9.770000 # loops : 120 mean,max change (kT/e) : 1.5569780E-03 4.7769547E-02 energy calculations done at 9.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.940000 DelPhi exited at 07:33:32 9.947u 0.338s 0:11.01 93.2% 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 Tue Oct 11 2011 at 07:33:32 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2569 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: 2.975870 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): 18.20800 71.05500 ymin,ymax (A): -34.50600 15.97400 zmin,zma (A): 5.984000 59.81700 x,y,z range (A): 52.84700 50.48000 53.83300 scale (grids/A): 2.975870 object centre (A): 44.63150 -9.266001 32.90050 number of atom coordinates read : 2569 total number of charged atoms : 2402 net assigned charge : -2.499994 assigned positive charge : 377.4972 centred at (gu) : 90.39634 77.62300 86.94111 assigned negative charge : -379.9977 centred at (gu) : 89.89557 77.30147 87.15763 start vw surface at 0.1600000 fill in re-entrant regions at 0.6300000 boundary points on vw surface= 191960 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20728 grid for indexing accessible points = 1.400000 m= 104644 mr = 144510 m= 41328 mr = 88598 m= 10691 mr = 34360 m= 1673 mr = 8469 m= 106 mr = 1238 m= 0 mr = 44 time to grow re-entrant surface = 1.210000 no. cavity mid-points inaccessible to solvent = 4769 time to turn everything in is 1.980000 number of dielectric boundary points 73183 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.140000 number of grid points assigned charge 19216 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) : 1.983913 object centre at (A) : 44.63150 -9.266001 32.90050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1249552 0.1765445 midg,1,midg; midg,igrid,midg 0.7051529 0.2321319 1,midg,midg; igrid,midg,midg 6.8280809E-02 -6.5484360E-02 gauss-seidel spectral radius is 0.9992816 estimated iterations to convergence 294 setup time was (sec) 2.320000 now iterating at: 07:33:35 rms-change max change #iterations 10.48851 368.1691 at 10iterations 6.149406 138.6371 at 20iterations 3.592873 64.17508 at 30iterations 2.095222 41.45638 at 40iterations 1.222927 20.25667 at 50iterations 0.7120445 12.00622 at 60iterations 0.4136828 7.503791 at 70iterations 0.2404410 4.507284 at 80iterations 0.1395063 2.308242 at 90iterations 8.1074812E-02 1.353996 at 100iterations 4.7074828E-02 0.7701035 at 110iterations 2.7330060E-02 0.4748077 at 120iterations 1.5835492E-02 0.2770557 at 130iterations 9.1965394E-03 0.1568375 at 140iterations 5.3356243E-03 8.4150314E-02 at 150iterations 3.1060113E-03 5.5159330E-02 at 160iterations 1.8109258E-03 3.2714844E-02 at 170iterations 1.0660933E-03 1.7772675E-02 at 180iterations finished qdiffx linear iterations at : 07:33:49 total time elapsed so far: 16.77000 # loops : 180 mean,max change (kT/e) : 1.0660933E-03 1.7772675E-02 energy calculations done at 16.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.96000 DelPhi exited at 07:33:50 16.957u 0.344s 0:17.68 97.7% 0+0k 0+0io 0pf+0w