Sat Oct 15 11:38:44 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 Sat Oct 15 2011 at 11:38:52 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2042 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6431333 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): 5.783000 61.13700 ymin,ymax (A): 2.910000 50.13400 zmin,zma (A): 14.67000 55.90400 x,y,z range (A): 55.35400 47.22400 41.23400 scale (grids/A): 0.6431333 object centre (A): 33.46000 26.52200 35.28700 number of atom coordinates read : 2042 total number of charged atoms : 1906 net assigned charge : 1.000005 assigned positive charge : 304.3427 centred at (gu) : 87.23173 89.40337 89.19546 assigned negative charge : -303.3429 centred at (gu) : 87.38258 89.42975 89.19225 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5669 nv = 96 ne = 84 npr = 41076 no. pairs analyzed = 41076 no. exposed pairs = 2594 no. arc points = 18498 no. surface atoms = 877 nbur = 1165 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 322 mr = 3047 m= 1 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 2911 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1666 ## 165 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 6599 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.3413655E-10 1.2135741E-09 midg,1,midg; midg,igrid,midg 4.2037165E-09 -1.2987758E-09 1,midg,midg; igrid,midg,midg 2.8875153E-08 -7.7022237E-09 gauss-seidel spectral radius is 0.9874246 estimated iterations to convergence 73 setup time was (sec) 0.5600000 now iterating at: 11:38:54 rms-change max change #iterations 0.1284305 20.86285 at 10iterations 1.2902425E-02 2.522968 at 20iterations 1.3140936E-03 0.1976089 at 30iterations 1.3225366E-04 2.0900249E-02 at 40iterations 1.5090494E-05 2.5405884E-03 at 50iterations finished qdiffx linear iterations at : 11:39:02 total time elapsed so far: 3.960000 # loops : 50 mean,max change (kT/e) : 1.5090494E-05 2.5405884E-03 energy calculations done at 3.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.140000 DelPhi exited at 11:39:03 4.147u 0.293s 0:11.91 37.1% 0+0k 0+0io 3pf+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 15 2011 at 11:39:04 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2042 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.929400 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): 5.783000 61.13700 ymin,ymax (A): 2.910000 50.13400 zmin,zma (A): 14.67000 55.90400 x,y,z range (A): 55.35400 47.22400 41.23400 scale (grids/A): 1.929400 object centre (A): 33.46000 26.52200 35.28700 number of atom coordinates read : 2042 total number of charged atoms : 1906 net assigned charge : 1.000005 assigned positive charge : 304.3427 centred at (gu) : 81.69519 88.21006 87.58644 assigned negative charge : -303.3429 centred at (gu) : 82.14769 88.28905 87.57658 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 61230 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18498 grid for indexing accessible points = 1.400000 m= 21521 mr = 41790 m= 3244 mr = 15370 m= 180 mr = 1919 m= 3 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 286 time to turn everything in is 0.5700000 number of dielectric boundary points 27071 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 116 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 15007 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) : 0.6431333 object centre at (A) : 33.46000 26.52200 35.28700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1101218E-03 1.7489127E-03 midg,1,midg; midg,igrid,midg 2.4577592E-02 1.4724124E-03 1,midg,midg; igrid,midg,midg -3.2755814E-02 -4.2267457E-02 gauss-seidel spectral radius is 0.9986095 estimated iterations to convergence 213 setup time was (sec) 0.9000000 now iterating at: 11:39:07 rms-change max change #iterations 3.799615 178.1194 at 10iterations 1.758489 60.12572 at 20iterations 0.8234587 29.47831 at 30iterations 0.3815823 13.39515 at 40iterations 0.1776344 6.138684 at 50iterations 8.2699016E-02 2.943947 at 60iterations 3.8328901E-02 1.434422 at 70iterations 1.7850058E-02 0.5917277 at 80iterations 8.3190864E-03 0.2879086 at 90iterations 3.8688411E-03 0.1363901 at 100iterations 1.7974217E-03 6.0989380E-02 at 110iterations 8.3885313E-04 3.0393600E-02 at 120iterations finished qdiffx linear iterations at : 11:39:32 total time elapsed so far: 9.370000 # loops : 120 mean,max change (kT/e) : 8.3885313E-04 3.0393600E-02 energy calculations done at 9.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.560000 DelPhi exited at 11:39:34 9.563u 0.303s 0:30.35 32.4% 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 Sat Oct 15 2011 at 11:39:36 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2042 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.894100 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): 5.783000 61.13700 ymin,ymax (A): 2.910000 50.13400 zmin,zma (A): 14.67000 55.90400 x,y,z range (A): 55.35400 47.22400 41.23400 scale (grids/A): 2.894100 object centre (A): 33.46000 26.52200 35.28700 number of atom coordinates read : 2042 total number of charged atoms : 1906 net assigned charge : 1.000005 assigned positive charge : 304.3427 centred at (gu) : 77.54274 87.31499 86.37952 assigned negative charge : -303.3429 centred at (gu) : 78.22138 87.43356 86.36488 start vw surface at 0.1500000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 141698 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18498 grid for indexing accessible points = 1.400000 m= 69938 mr = 101592 m= 24467 mr = 56295 m= 5788 mr = 19217 m= 784 mr = 4104 m= 26 mr = 458 m= 0 mr = 4 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 1072 time to turn everything in is 1.430000 number of dielectric boundary points 61031 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 15244 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) : 1.929400 object centre at (A) : 33.46000 26.52200 35.28700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4802127E-02 8.0686985E-03 midg,1,midg; midg,igrid,midg 0.2714153 -4.6779528E-02 1,midg,midg; igrid,midg,midg -0.6517882 -0.7219552 gauss-seidel spectral radius is 0.9992417 estimated iterations to convergence 287 setup time was (sec) 1.760000 now iterating at: 11:39:44 rms-change max change #iterations 8.977304 376.1686 at 10iterations 5.223002 125.2324 at 20iterations 3.021154 68.55873 at 30iterations 1.748669 37.19012 at 40iterations 1.006809 23.50636 at 50iterations 0.5785536 12.49480 at 60iterations 0.3317472 7.064503 at 70iterations 0.1903899 4.076681 at 80iterations 0.1089424 2.155939 at 90iterations 6.2460281E-02 1.313677 at 100iterations 3.5686757E-02 0.6884575 at 110iterations 2.0364277E-02 0.4628525 at 120iterations 1.1646949E-02 0.2393079 at 130iterations 6.6515664E-03 0.1268477 at 140iterations 3.8022026E-03 7.4195862E-02 at 150iterations 2.1743348E-03 4.3312073E-02 at 160iterations 1.2443555E-03 2.3796082E-02 at 170iterations 7.1345182E-04 1.4022827E-02 at 180iterations finished qdiffx linear iterations at : 11:40:16 total time elapsed so far: 15.55000 # loops : 180 mean,max change (kT/e) : 7.1345182E-04 1.4022827E-02 energy calculations done at 15.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.74000 DelPhi exited at 11:40:17 15.737u 0.287s 0:42.02 38.1% 0+0k 0+0io 0pf+0w