Tue Oct 11 03:41:26 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 03:41:27 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: 344 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2802 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 0.6352832 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): -10.93600 36.99300 ymin,ymax (A): -26.93700 23.34700 zmin,zma (A): -10.76300 45.27500 x,y,z range (A): 47.92900 50.28400 56.03800 scale (grids/A): 0.6352832 object centre (A): 13.02850 -1.795000 17.25600 number of atom coordinates read : 2802 total number of charged atoms : 2639 net assigned charge : 1.566024 assigned positive charge : 426.7697 centred at (gu) : 89.89658 90.06429 91.93307 assigned negative charge : -425.2042 centred at (gu) : 89.68321 89.93630 91.89922 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7395 nv = 96 ne = 84 npr = 57450 no. pairs analyzed = 57450 no. exposed pairs = 3359 no. arc points = 23137 no. surface atoms = 1127 nbur = 1675 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 358 mr = 4168 m= 2 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.3300000 number of dielectric boundary points 3538 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2286 ## 211 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 9033 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1828957E-09 8.7340082E-09 midg,1,midg; midg,igrid,midg -1.2386381E-08 1.6299698E-08 1,midg,midg; igrid,midg,midg -2.3000608E-08 2.4707489E-08 gauss-seidel spectral radius is 0.9871742 estimated iterations to convergence 72 setup time was (sec) 0.6300000 now iterating at: 03:41:27 rms-change max change #iterations 0.1481787 21.02307 at 10iterations 1.4489350E-02 1.988115 at 20iterations 1.4648230E-03 0.2441616 at 30iterations 1.6081460E-04 2.4276733E-02 at 40iterations 2.2838773E-05 3.1585693E-03 at 50iterations finished qdiffx linear iterations at : 03:41:31 total time elapsed so far: 4.340000 # loops : 50 mean,max change (kT/e) : 2.2838773E-05 3.1585693E-03 energy calculations done at 4.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.520000 DelPhi exited at 03:41:32 4.521u 0.378s 0:05.84 83.7% 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 03:41:32 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: 344 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2802 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 1.905850 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): -10.93600 36.99300 ymin,ymax (A): -26.93700 23.34700 zmin,zma (A): -10.76300 45.27500 x,y,z range (A): 47.92900 50.28400 56.03800 scale (grids/A): 1.905850 object centre (A): 13.02850 -1.795000 17.25600 number of atom coordinates read : 2802 total number of charged atoms : 2639 net assigned charge : 1.566024 assigned positive charge : 426.7697 centred at (gu) : 89.68957 90.19240 95.79866 assigned negative charge : -425.2042 centred at (gu) : 89.04905 89.80852 95.69714 start vw surface at 0.1300000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 80254 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23137 grid for indexing accessible points = 1.400000 m= 28301 mr = 56772 m= 4087 mr = 20919 m= 205 mr = 2496 m= 2 mr = 85 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 1922 time to turn everything in is 0.6400000 number of dielectric boundary points 32577 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 126 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 20723 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) : 0.6352832 object centre at (A) : 13.02850 -1.795000 17.25600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.6714997E-02 4.0081874E-03 midg,1,midg; midg,igrid,midg -1.8281616E-02 -3.5392358E-03 1,midg,midg; igrid,midg,midg -9.8286122E-03 4.9798522E-02 gauss-seidel spectral radius is 0.9986516 estimated iterations to convergence 216 setup time was (sec) 1.010000 now iterating at: 03:41:34 rms-change max change #iterations 4.509183 188.8746 at 10iterations 2.122549 67.33683 at 20iterations 1.003071 32.37133 at 30iterations 0.4742322 14.97211 at 40iterations 0.2234817 6.832513 at 50iterations 0.1054576 3.238197 at 60iterations 4.9733154E-02 1.804610 at 70iterations 2.3349173E-02 0.6856441 at 80iterations 1.1062934E-02 0.3489587 at 90iterations 5.2142194E-03 0.1717644 at 100iterations 2.4607808E-03 7.4274063E-02 at 110iterations 1.1658827E-03 3.4331322E-02 at 120iterations finished qdiffx linear iterations at : 03:41:43 total time elapsed so far: 10.71000 # loops : 120 mean,max change (kT/e) : 1.1658827E-03 3.4331322E-02 energy calculations done at 10.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.87000 DelPhi exited at 03:41:44 10.873u 0.428s 0:11.72 96.3% 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 Tue Oct 11 2011 at 03:41:44 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: 344 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2802 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 2.858774 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): -10.93600 36.99300 ymin,ymax (A): -26.93700 23.34700 zmin,zma (A): -10.76300 45.27500 x,y,z range (A): 47.92900 50.28400 56.03800 scale (grids/A): 2.858774 object centre (A): 13.02850 -1.795000 17.25600 number of atom coordinates read : 2802 total number of charged atoms : 2639 net assigned charge : 1.566024 assigned positive charge : 426.7697 centred at (gu) : 89.53428 90.28844 98.69775 assigned negative charge : -425.2042 centred at (gu) : 88.57356 89.71276 98.54563 start vw surface at 0.1200000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 185721 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23137 grid for indexing accessible points = 1.400000 m= 93250 mr = 137421 m= 32045 mr = 76627 m= 7302 mr = 25710 m= 960 mr = 5537 m= 54 mr = 636 m= 3 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 6644 time to turn everything in is 1.670000 number of dielectric boundary points 73372 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.810000 number of grid points assigned charge 21108 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) : 1.905850 object centre at (A) : 13.02850 -1.795000 17.25600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5381260 0.2578771 midg,1,midg; midg,igrid,midg -0.2140319 -0.1346770 1,midg,midg; igrid,midg,midg -4.1611090E-02 0.4754536 gauss-seidel spectral radius is 0.9992626 estimated iterations to convergence 291 setup time was (sec) 2.000000 now iterating at: 03:41:47 rms-change max change #iterations 10.43567 349.8324 at 10iterations 6.088992 131.6186 at 20iterations 3.546212 75.20286 at 30iterations 2.054913 38.50064 at 40iterations 1.191432 21.55482 at 50iterations 0.6884852 12.89646 at 60iterations 0.3974947 7.014999 at 70iterations 0.2296538 4.955829 at 80iterations 0.1326458 2.456249 at 90iterations 7.6408431E-02 1.456341 at 100iterations 4.4165146E-02 0.7962208 at 110iterations 2.5466753E-02 0.4798546 at 120iterations 1.4669902E-02 0.2565765 at 130iterations 8.4701786E-03 0.1541138 at 140iterations 4.8936629E-03 8.7818146E-02 at 150iterations 2.8491900E-03 4.7653198E-02 at 160iterations 1.6597185E-03 2.8747559E-02 at 170iterations 9.7527081E-04 1.7234802E-02 at 180iterations finished qdiffx linear iterations at : 03:42:03 total time elapsed so far: 17.86000 # loops : 180 mean,max change (kT/e) : 9.7527081E-04 1.7234802E-02 energy calculations done at 17.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.03000 DelPhi exited at 03:42:03 18.036u 0.473s 0:18.88 97.9% 0+0k 0+0io 0pf+0w