Sat Oct 8 21:46:31 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 21:46:31 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 = 2038 !!! WARNING: HIR 121 has a net charge of 0.5140 !!! WARNING: GLM 161 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6646379 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): 6.341000 59.90400 ymin,ymax (A): 2.891000 50.08300 zmin,zma (A): 13.35500 56.01900 x,y,z range (A): 53.56300 47.19200 42.66400 scale (grids/A): 0.6646379 object centre (A): 33.12250 26.48700 34.68700 number of atom coordinates read : 2038 total number of charged atoms : 1898 net assigned charge : 0.9200036 assigned positive charge : 304.9348 centred at (gu) : 87.72930 89.35706 89.35505 assigned negative charge : -304.0148 centred at (gu) : 87.87093 89.43268 89.40284 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6082 nv = 96 ne = 84 npr = 41089 no. pairs analyzed = 41089 no. exposed pairs = 2574 no. arc points = 18445 no. surface atoms = 863 nbur = 1175 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 379 mr = 3340 m= 1 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 16 time to turn everything in is 0.1600000 number of dielectric boundary points 3065 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1710 ## 185 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 6982 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1585473E-08 -5.6163940E-09 midg,1,midg; midg,igrid,midg 1.7038788E-08 -9.8895958E-09 1,midg,midg; igrid,midg,midg 4.2276152E-08 -1.4322599E-08 gauss-seidel spectral radius is 0.9882160 estimated iterations to convergence 75 setup time was (sec) 0.3600000 now iterating at: 21:46:31 rms-change max change #iterations 0.1531086 25.79219 at 10iterations 1.6402563E-02 2.671551 at 20iterations 1.7834130E-03 0.2762756 at 30iterations 1.8950184E-04 2.7442932E-02 at 40iterations 2.1530339E-05 3.0612946E-03 at 50iterations finished qdiffx linear iterations at : 21:46:34 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 2.1530339E-05 3.0612946E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 21:46:35 3.333u 0.152s 0:03.74 93.0% 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 21:46:35 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 = 2038 !!! WARNING: HIR 121 has a net charge of 0.5140 !!! WARNING: GLM 161 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.993914 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): 6.341000 59.90400 ymin,ymax (A): 2.891000 50.08300 zmin,zma (A): 13.35500 56.01900 x,y,z range (A): 53.56300 47.19200 42.66400 scale (grids/A): 1.993914 object centre (A): 33.12250 26.48700 34.68700 number of atom coordinates read : 2038 total number of charged atoms : 1898 net assigned charge : 0.9200036 assigned positive charge : 304.9348 centred at (gu) : 83.18780 88.07076 88.06509 assigned negative charge : -304.0148 centred at (gu) : 83.61272 88.29794 88.20824 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 65073 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18445 grid for indexing accessible points = 1.400000 m= 23914 mr = 44622 m= 4438 mr = 17538 m= 337 mr = 2973 m= 5 mr = 139 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 1733 time to turn everything in is 0.3300000 number of dielectric boundary points 28495 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 92 iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 14986 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) : 0.6646379 object centre at (A) : 33.12250 26.48700 34.68700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1718856E-02 -1.1614509E-03 midg,1,midg; midg,igrid,midg 3.4278262E-02 1.0965060E-03 1,midg,midg; igrid,midg,midg -3.3550568E-02 -4.3061223E-02 gauss-seidel spectral radius is 0.9986932 estimated iterations to convergence 219 setup time was (sec) 0.5400000 now iterating at: 21:46:35 rms-change max change #iterations 4.117932 194.1472 at 10iterations 1.950503 71.82301 at 20iterations 0.9284442 31.91655 at 30iterations 0.4433250 16.62163 at 40iterations 0.2110537 7.049799 at 50iterations 0.1003601 3.207691 at 60iterations 4.7759339E-02 1.589024 at 70iterations 2.2729335E-02 0.7185659 at 80iterations 1.0801473E-02 0.3769226 at 90iterations 5.1449584E-03 0.1778040 at 100iterations 2.4583833E-03 8.4003448E-02 at 110iterations 1.1727889E-03 4.0143967E-02 at 120iterations finished qdiffx linear iterations at : 21:46:42 total time elapsed so far: 7.520000 # loops : 120 mean,max change (kT/e) : 1.1727889E-03 4.0143967E-02 energy calculations done at 7.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.660000 DelPhi exited at 21:46:43 7.664u 0.179s 0:08.10 96.6% 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 Sat Oct 8 2011 at 21:46:43 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 = 2038 !!! WARNING: HIR 121 has a net charge of 0.5140 !!! WARNING: GLM 161 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.990870 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): 6.341000 59.90400 ymin,ymax (A): 2.891000 50.08300 zmin,zma (A): 13.35500 56.01900 x,y,z range (A): 53.56300 47.19200 42.66400 scale (grids/A): 2.990870 object centre (A): 33.12250 26.48700 34.68700 number of atom coordinates read : 2038 total number of charged atoms : 1898 net assigned charge : 0.9200036 assigned positive charge : 304.9348 centred at (gu) : 79.78158 87.10620 87.09769 assigned negative charge : -304.0148 centred at (gu) : 80.41906 87.44680 87.31236 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 150391 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18445 grid for indexing accessible points = 1.400000 m= 75780 mr = 108204 m= 29071 mr = 61669 m= 8257 mr = 23445 m= 1508 mr = 6411 m= 85 mr = 1115 m= 1 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 6086 time to turn everything in is 0.8500000 number of dielectric boundary points 64201 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 15184 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) : 1.993914 object centre at (A) : 33.12250 26.48700 34.68700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1392861 -1.6817110E-02 midg,1,midg; midg,igrid,midg 0.3001733 -6.7843415E-02 1,midg,midg; igrid,midg,midg -0.5658741 -0.5384158 gauss-seidel spectral radius is 0.9992645 estimated iterations to convergence 291 setup time was (sec) 1.080000 now iterating at: 21:46:44 rms-change max change #iterations 9.496495 394.8076 at 10iterations 5.575210 134.4873 at 20iterations 3.250481 69.79423 at 30iterations 1.890123 39.85582 at 40iterations 1.097973 24.88873 at 50iterations 0.6358097 12.30442 at 60iterations 0.3678645 7.723534 at 70iterations 0.2130283 4.060657 at 80iterations 0.1230884 2.636364 at 90iterations 7.0902579E-02 1.338776 at 100iterations 4.0889263E-02 0.7645569 at 110iterations 2.3520440E-02 0.4967117 at 120iterations 1.3565069E-02 0.2549686 at 130iterations 7.8260731E-03 0.1462498 at 140iterations 4.5112818E-03 8.9221001E-02 at 150iterations 2.5980170E-03 4.9087524E-02 at 160iterations 1.4950186E-03 2.8430223E-02 at 170iterations 8.5914857E-04 1.6791821E-02 at 180iterations finished qdiffx linear iterations at : 21:46:55 total time elapsed so far: 12.15000 # loops : 180 mean,max change (kT/e) : 8.5914857E-04 1.6791821E-02 energy calculations done at 12.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.29000 DelPhi exited at 21:46:56 12.290u 0.189s 0:12.74 97.8% 0+0k 0+0io 0pf+0w