Thu Jan 19 13:32:26 PST 2012 #!/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 Thu Jan 19 2012 at 13:32:30 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: 346 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6831 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1105 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.4371048 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): -2.365000 79.08000 ymin,ymax (A): -12.14400 67.37600 zmin,zma (A): -23.32600 42.03400 x,y,z range (A): 81.44500 79.52000 65.36000 scale (grids/A): 0.4371048 object centre (A): 38.35750 27.61600 9.354000 number of atom coordinates read : 6831 total number of charged atoms : 6660 net assigned charge : 2.200046 assigned positive charge : 1046.097 centred at (gu) : 88.11275 90.20444 89.98494 assigned negative charge : -1043.906 centred at (gu) : 88.03303 90.26179 89.90298 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7720 nv = 96 ne = 84 npr = 137211 no. pairs analyzed = 137211 no. exposed pairs = 8865 no. arc points = 60737 no. surface atoms = 2952 nbur = 3879 mkacc time = 0.2400000 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 = 1.904000 m= 213 mr = 3630 m= 0 mr = 2 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.4300000 number of dielectric boundary points 4301 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5186 ## 1089 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 10752 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.1488492E-12 8.6070222E-12 midg,1,midg; midg,igrid,midg 5.9453991E-12 -5.0058178E-12 1,midg,midg; igrid,midg,midg -1.2464153E-11 4.7522034E-12 gauss-seidel spectral radius is 0.9734369 estimated iterations to convergence 51 setup time was (sec) 0.6200000 now iterating at: 13:32:33 rms-change max change #iterations 3.2647971E-02 4.772202 at 10iterations 1.6844368E-03 0.3068600 at 20iterations 4.4474372E-04 6.0790062E-02 at 30iterations 1.5971264E-04 2.1156311E-02 at 40iterations 5.8022262E-05 7.6198578E-03 at 50iterations finished qdiffx linear iterations at : 13:32:43 total time elapsed so far: 3.630000 # loops : 50 mean,max change (kT/e) : 5.8022262E-05 7.6198578E-03 energy calculations done at 3.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.760000 DelPhi exited at 13:32:44 3.761u 0.203s 0:14.50 27.3% 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 Thu Jan 19 2012 at 13:32:46 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: 346 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6831 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1105 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.311314 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): -2.365000 79.08000 ymin,ymax (A): -12.14400 67.37600 zmin,zma (A): -23.32600 42.03400 x,y,z range (A): 81.44500 79.52000 65.36000 scale (grids/A): 1.311314 object centre (A): 38.35750 27.61600 9.354000 number of atom coordinates read : 6831 total number of charged atoms : 6660 net assigned charge : 2.200046 assigned positive charge : 1046.097 centred at (gu) : 84.33611 90.61182 89.95307 assigned negative charge : -1043.906 centred at (gu) : 84.09873 90.78486 89.70850 start vw surface at 0.1700000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 90556 reading accessible surface arcs data from file ARCDAT no. of arc points read = 60737 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.792000 m= 20221 mr = 59416 m= 1015 mr = 11684 m= 5 mr = 227 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 630 time to turn everything in is 0.4900000 number of dielectric boundary points 40470 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1216 ## 53 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 46664 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) : 0.4371048 object centre at (A) : 38.35750 27.61600 9.354000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.8860419E-03 2.5578029E-03 midg,1,midg; midg,igrid,midg 8.6052017E-03 4.0188255E-03 1,midg,midg; igrid,midg,midg -1.7168192E-02 3.5838513E-03 gauss-seidel spectral radius is 0.9975095 estimated iterations to convergence 160 setup time was (sec) 0.7300000 now iterating at: 13:32:50 rms-change max change #iterations 3.238172 171.4484 at 10iterations 1.160448 46.99905 at 20iterations 0.4162218 13.92888 at 30iterations 0.1496257 4.683114 at 40iterations 5.3990308E-02 1.747591 at 50iterations 1.9444602E-02 0.7416625 at 60iterations 7.1420930E-03 0.2446785 at 70iterations 2.7120644E-03 0.1068468 at 80iterations 1.1365551E-03 3.7634850E-02 at 90iterations 5.7132466E-04 1.9119024E-02 at 100iterations 3.4476057E-04 1.0747671E-02 at 110iterations 2.2679231E-04 6.2236786E-03 at 120iterations finished qdiffx linear iterations at : 13:33:08 total time elapsed so far: 8.110000 # loops : 120 mean,max change (kT/e) : 2.2679231E-04 6.2236786E-03 energy calculations done at 8.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.250000 DelPhi exited at 13:33:10 8.254u 0.205s 0:24.41 34.6% 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 Thu Jan 19 2012 at 13:33:12 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: 346 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6831 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1105 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.966972 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): -2.365000 79.08000 ymin,ymax (A): -12.14400 67.37600 zmin,zma (A): -23.32600 42.03400 x,y,z range (A): 81.44500 79.52000 65.36000 scale (grids/A): 1.966972 object centre (A): 38.35750 27.61600 9.354000 number of atom coordinates read : 6831 total number of charged atoms : 6660 net assigned charge : 2.200046 assigned positive charge : 1046.097 centred at (gu) : 81.50372 90.91726 89.92924 assigned negative charge : -1043.906 centred at (gu) : 81.14815 91.17727 89.56273 start vw surface at 0.1700000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 212366 reading accessible surface arcs data from file ARCDAT no. of arc points read = 60737 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.764000 m= 80123 mr = 148688 m= 13535 mr = 58328 m= 1008 mr = 8311 m= 21 mr = 415 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 2019 time to turn everything in is 1.170000 number of dielectric boundary points 91311 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 371 ## 1 charges are in solution ## iepsmp to db, and charging done at 1.300000 number of grid points assigned charge 52652 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) : 1.311314 object centre at (A) : 38.35750 27.61600 9.354000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.2398979E-02 6.5590262E-02 midg,1,midg; midg,igrid,midg 0.2654336 0.1068585 1,midg,midg; igrid,midg,midg -0.5819229 0.1252690 gauss-seidel spectral radius is 0.9990208 estimated iterations to convergence 253 setup time was (sec) 1.500000 now iterating at: 13:33:20 rms-change max change #iterations 9.828573 288.9622 at 10iterations 5.395154 128.7387 at 20iterations 2.944572 73.04663 at 30iterations 1.590754 39.07450 at 40iterations 0.8540519 20.21035 at 50iterations 0.4583306 10.88169 at 60iterations 0.2456490 5.340481 at 70iterations 0.1306322 3.076188 at 80iterations 6.9682337E-02 1.607044 at 90iterations 3.7129082E-02 0.8126888 at 100iterations 1.9711668E-02 0.4232454 at 110iterations 1.0452854E-02 0.2238922 at 120iterations 5.5526458E-03 0.1185589 at 130iterations 2.9498513E-03 7.1716309E-02 at 140iterations 1.5663118E-03 3.4240723E-02 at 150iterations 8.3386601E-04 1.8474579E-02 at 160iterations 4.4631900E-04 8.8272095E-03 at 170iterations 2.4058425E-04 5.4550171E-03 at 180iterations finished qdiffx linear iterations at : 13:33:48 total time elapsed so far: 14.96000 # loops : 180 mean,max change (kT/e) : 2.4058425E-04 5.4550171E-03 energy calculations done at 14.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.09000 DelPhi exited at 13:33:49 15.095u 0.315s 0:37.26 41.3% 0+0k 0+0io 0pf+0w