Tue Oct 11 04:22:16 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+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 Tue Oct 11 2011 at 04:22:16 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2760 !!! 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6748304 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): -14.96100 32.88100 ymin,ymax (A): 7.004000 55.43700 zmin,zma (A): 25.32400 78.07800 x,y,z range (A): 47.84200 48.43300 52.75399 scale (grids/A): 0.6748304 object centre (A): 8.960001 31.22050 51.70100 number of atom coordinates read : 2760 total number of charged atoms : 2608 net assigned charge : 3.140015 assigned positive charge : 416.3456 centred at (gu) : 90.34041 90.50133 88.82393 assigned negative charge : -413.2063 centred at (gu) : 90.66607 90.32632 88.77316 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8436 nv = 96 ne = 84 npr = 56757 no. pairs analyzed = 56757 no. exposed pairs = 3386 no. arc points = 23570 no. surface atoms = 1133 nbur = 1627 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 490 mr = 4789 m= 4 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 60 time to turn everything in is 0.3100000 number of dielectric boundary points 4068 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2237 ## 207 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 9792 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.3613269E-09 2.1868050E-08 midg,1,midg; midg,igrid,midg -3.7805730E-08 7.1792080E-08 1,midg,midg; igrid,midg,midg 1.0100085E-07 -9.7163863E-08 gauss-seidel spectral radius is 0.9886277 estimated iterations to convergence 76 setup time was (sec) 0.5200000 now iterating at: 04:22:17 rms-change max change #iterations 0.1841955 25.05427 at 10iterations 2.0890580E-02 3.017944 at 20iterations 2.3610115E-03 0.3090973 at 30iterations 2.8309104E-04 3.5503387E-02 at 40iterations 3.9475945E-05 5.0086975E-03 at 50iterations finished qdiffx linear iterations at : 04:22:19 total time elapsed so far: 2.980000 # loops : 50 mean,max change (kT/e) : 3.9475945E-05 5.0086975E-03 energy calculations done at 2.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.160000 DelPhi exited at 04:22:20 3.164u 0.173s 0:03.66 90.9% 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 04:22:20 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2760 !!! 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.024491 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): -14.96100 32.88100 ymin,ymax (A): 7.004000 55.43700 zmin,zma (A): 25.32400 78.07800 x,y,z range (A): 47.84200 48.43300 52.75399 scale (grids/A): 2.024491 object centre (A): 8.960001 31.22050 51.70100 number of atom coordinates read : 2760 total number of charged atoms : 2608 net assigned charge : 3.140015 assigned positive charge : 416.3456 centred at (gu) : 91.02045 91.50342 86.47121 assigned negative charge : -413.2063 centred at (gu) : 91.99808 90.97855 86.31919 start vw surface at 0.2100000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 90486 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23570 grid for indexing accessible points = 1.400000 m= 34764 mr = 64284 m= 6019 mr = 26181 m= 395 mr = 3909 m= 4 mr = 149 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1624 time to turn everything in is 0.7000000 number of dielectric boundary points 37145 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 111 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 20626 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) : 0.6748304 object centre at (A) : 8.960001 31.22050 51.70100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1148469E-02 1.0839907E-02 midg,1,midg; midg,igrid,midg -1.7794821E-02 4.8409194E-02 1,midg,midg; igrid,midg,midg 8.7655224E-02 -3.1752769E-02 gauss-seidel spectral radius is 0.9987987 estimated iterations to convergence 228 setup time was (sec) 0.9900000 now iterating at: 04:22:21 rms-change max change #iterations 4.965318 193.9773 at 10iterations 2.438931 74.54743 at 20iterations 1.196092 38.77982 at 30iterations 0.5904054 18.01164 at 40iterations 0.2892761 8.370802 at 50iterations 0.1426529 4.156718 at 60iterations 7.0038594E-02 2.152992 at 70iterations 3.4520604E-02 1.119062 at 80iterations 1.6925862E-02 0.5012112 at 90iterations 8.3294017E-03 0.2382393 at 100iterations 4.1001514E-03 0.1153812 at 110iterations 2.0137893E-03 5.9570313E-02 at 120iterations finished qdiffx linear iterations at : 04:22:27 total time elapsed so far: 7.460000 # loops : 120 mean,max change (kT/e) : 2.0137893E-03 5.9570313E-02 energy calculations done at 7.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.640000 DelPhi exited at 04:22:28 7.645u 0.201s 0:08.39 93.4% 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 Tue Oct 11 2011 at 04:22:28 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2760 !!! 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 3.036737 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): -14.96100 32.88100 ymin,ymax (A): 7.004000 55.43700 zmin,zma (A): 25.32400 78.07800 x,y,z range (A): 47.84200 48.43300 52.75399 scale (grids/A): 3.036737 object centre (A): 8.960001 31.22050 51.70100 number of atom coordinates read : 2760 total number of charged atoms : 2608 net assigned charge : 3.140015 assigned positive charge : 416.3456 centred at (gu) : 91.53053 92.25490 84.70668 assigned negative charge : -413.2063 centred at (gu) : 92.99687 91.46786 84.47863 start vw surface at 0.2200000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 209104 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23570 grid for indexing accessible points = 1.400000 m= 110455 mr = 154902 m= 42442 mr = 91787 m= 11038 mr = 34684 m= 1830 mr = 8522 m= 141 mr = 1284 m= 2 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 5310 time to turn everything in is 1.700000 number of dielectric boundary points 83771 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.830000 number of grid points assigned charge 20862 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) : 2.024491 object centre at (A) : 8.960001 31.22050 51.70100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1378807 1.9186990E-02 midg,1,midg; midg,igrid,midg -0.1787014 0.5416958 1,midg,midg; igrid,midg,midg 0.7083680 -0.1712548 gauss-seidel spectral radius is 0.9992983 estimated iterations to convergence 298 setup time was (sec) 1.990000 now iterating at: 04:22:30 rms-change max change #iterations 11.29014 567.9342 at 10iterations 6.680041 133.0538 at 20iterations 3.948876 79.71910 at 30iterations 2.327477 45.69235 at 40iterations 1.370346 25.93576 at 50iterations 0.8063250 14.54406 at 60iterations 0.4735574 8.352530 at 70iterations 0.2783302 5.139990 at 80iterations 0.1628888 2.778303 at 90iterations 9.5581800E-02 1.641112 at 100iterations 5.5894800E-02 1.017748 at 110iterations 3.2714412E-02 0.5426187 at 120iterations 1.9182177E-02 0.3482571 at 130iterations 1.1204073E-02 0.1887884 at 140iterations 6.5888236E-03 0.1120377 at 150iterations 3.8693715E-03 6.6020966E-02 at 160iterations 2.2919725E-03 4.0998459E-02 at 170iterations 1.3665525E-03 2.2407532E-02 at 180iterations finished qdiffx linear iterations at : 04:22:41 total time elapsed so far: 12.56000 # loops : 180 mean,max change (kT/e) : 1.3665525E-03 2.2407532E-02 energy calculations done at 12.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.73000 DelPhi exited at 04:22:42 12.736u 0.238s 0:13.49 96.0% 0+0k 0+0io 0pf+0w