Sat Oct 8 18:47:53 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 Sat Oct 8 2011 at 18:47:53 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2581 !!! WARNING: HIR 64 has a net charge of 0.5140 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 459 has a net charge of 1.4000 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: 0.6331702 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): -32.11000 17.55700 ymin,ymax (A): -23.78000 23.20500 zmin,zma (A): -11.44600 44.77900 x,y,z range (A): 49.66700 46.98500 56.22500 scale (grids/A): 0.6331702 object centre (A): -7.276501 -0.2874994 16.66650 number of atom coordinates read : 2581 total number of charged atoms : 2450 net assigned charge : 3.920007 assigned positive charge : 392.6860 centred at (gu) : 88.56980 89.19237 89.41875 assigned negative charge : -388.7665 centred at (gu) : 88.48675 89.22710 89.30454 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6895 nv = 96 ne = 84 npr = 53318 no. pairs analyzed = 53318 no. exposed pairs = 2976 no. arc points = 21312 no. surface atoms = 1005 nbur = 1576 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 351 mr = 3905 m= 2 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 89 time to turn everything in is 0.2800000 number of dielectric boundary points 3293 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2205 ## 216 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8368 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.2152271E-09 1.3873773E-08 midg,1,midg; midg,igrid,midg 9.7370059E-09 1.2799456E-09 1,midg,midg; igrid,midg,midg -4.5640687E-09 9.4150270E-09 gauss-seidel spectral radius is 0.9870747 estimated iterations to convergence 72 setup time was (sec) 0.4900000 now iterating at: 18:47:54 rms-change max change #iterations 0.1412649 20.20969 at 10iterations 1.3651127E-02 1.960758 at 20iterations 1.3447705E-03 0.1839738 at 30iterations 1.2781553E-04 1.8404007E-02 at 40iterations 1.2623840E-05 1.8596649E-03 at 50iterations finished qdiffx linear iterations at : 18:47:56 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 1.2623840E-05 1.8596649E-03 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.120000 DelPhi exited at 18:47:57 3.122u 0.157s 0:03.55 92.1% 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 Sat Oct 8 2011 at 18:47:57 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2581 !!! WARNING: HIR 64 has a net charge of 0.5140 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 459 has a net charge of 1.4000 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: 1.899511 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): -32.11000 17.55700 ymin,ymax (A): -23.78000 23.20500 zmin,zma (A): -11.44600 44.77900 x,y,z range (A): 49.66700 46.98500 56.22500 scale (grids/A): 1.899511 object centre (A): -7.276501 -0.2874994 16.66650 number of atom coordinates read : 2581 total number of charged atoms : 2450 net assigned charge : 3.920007 assigned positive charge : 392.6860 centred at (gu) : 85.70877 87.57662 88.25577 assigned negative charge : -388.7665 centred at (gu) : 85.45995 87.68104 87.91351 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 74519 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21312 grid for indexing accessible points = 1.400000 m= 27450 mr = 52512 m= 4351 mr = 20784 m= 247 mr = 2776 m= 2 mr = 98 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 2463 time to turn everything in is 0.5200000 number of dielectric boundary points 30399 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 152 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 19273 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) : 0.6331702 object centre at (A) : -7.276501 -0.2874994 16.66650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3853431E-02 2.4510426E-02 midg,1,midg; midg,igrid,midg 1.4093149E-02 3.5193199E-03 1,midg,midg; igrid,midg,midg -4.2913184E-03 3.5016686E-02 gauss-seidel spectral radius is 0.9986234 estimated iterations to convergence 214 setup time was (sec) 0.7800000 now iterating at: 18:47:58 rms-change max change #iterations 4.248361 174.0999 at 10iterations 1.984039 64.98361 at 20iterations 0.9274652 29.67979 at 30iterations 0.4339802 15.92087 at 40iterations 0.2020388 6.774546 at 50iterations 9.4568923E-02 3.187353 at 60iterations 4.4225134E-02 1.358913 at 70iterations 2.0695396E-02 0.6562300 at 80iterations 9.6412264E-03 0.3006191 at 90iterations 4.5086634E-03 0.1450710 at 100iterations 2.1056342E-03 7.2086334E-02 at 110iterations 9.8414521E-04 3.3695221E-02 at 120iterations finished qdiffx linear iterations at : 18:48:04 total time elapsed so far: 6.740000 # loops : 120 mean,max change (kT/e) : 9.8414521E-04 3.3695221E-02 energy calculations done at 6.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.910000 DelPhi exited at 18:48:04 6.913u 0.187s 0:07.38 96.0% 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 Sat Oct 8 2011 at 18:48:04 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2581 !!! WARNING: HIR 64 has a net charge of 0.5140 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 459 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.849266 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): -32.11000 17.55700 ymin,ymax (A): -23.78000 23.20500 zmin,zma (A): -11.44600 44.77900 x,y,z range (A): 49.66700 46.98500 56.22500 scale (grids/A): 2.849266 object centre (A): -7.276501 -0.2874994 16.66650 number of atom coordinates read : 2581 total number of charged atoms : 2450 net assigned charge : 3.920007 assigned positive charge : 392.6860 centred at (gu) : 83.56320 86.36488 87.38363 assigned negative charge : -388.7665 centred at (gu) : 83.18983 86.52155 86.87037 start vw surface at 0.1400000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 172420 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21312 grid for indexing accessible points = 1.400000 m= 88851 mr = 126840 m= 32468 mr = 74073 m= 7770 mr = 26529 m= 1152 mr = 5984 m= 62 mr = 787 m= 0 mr = 29 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 8266 time to turn everything in is 1.280000 number of dielectric boundary points 68481 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.410000 number of grid points assigned charge 19599 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) : 1.899511 object centre at (A) : -7.276501 -0.2874994 16.66650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1165656 0.3355339 midg,1,midg; midg,igrid,midg 0.1677345 1.7428702E-02 1,midg,midg; igrid,midg,midg -1.3809405E-02 0.4393145 gauss-seidel spectral radius is 0.9992502 estimated iterations to convergence 288 setup time was (sec) 1.560000 now iterating at: 18:48:06 rms-change max change #iterations 9.853169 391.2515 at 10iterations 5.710227 140.5898 at 20iterations 3.290406 62.13952 at 30iterations 1.890791 36.96886 at 40iterations 1.085625 20.78556 at 50iterations 0.6233518 11.74966 at 60iterations 0.3570531 6.692978 at 70iterations 0.2047949 4.035971 at 80iterations 0.1173010 2.181435 at 90iterations 6.7088328E-02 1.253052 at 100iterations 3.8466673E-02 0.7546654 at 110iterations 2.2012023E-02 0.3971863 at 120iterations 1.2594256E-02 0.2228432 at 130iterations 7.1872468E-03 0.1302052 at 140iterations 4.1200062E-03 7.7936172E-02 at 150iterations 2.3579788E-03 4.2140961E-02 at 160iterations 1.3519893E-03 3.2048225E-02 at 170iterations 7.7276205E-04 1.4850616E-02 at 180iterations finished qdiffx linear iterations at : 18:48:16 total time elapsed so far: 11.01000 # loops : 180 mean,max change (kT/e) : 7.7276205E-04 1.4850616E-02 energy calculations done at 11.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.19000 DelPhi exited at 18:48:16 11.190u 0.192s 0:11.66 97.5% 0+0k 0+0io 0pf+0w