Sun Oct 16 14:31:24 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 Sun Oct 16 2011 at 14:31:29 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 = 2242 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 0.6382216 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): -0.1830000 53.16400 ymin,ymax (A): -16.48900 27.53400 zmin,zma (A): 28.60200 84.38200 x,y,z range (A): 53.34700 44.02300 55.78000 scale (grids/A): 0.6382216 object centre (A): 26.49050 5.522500 56.49200 number of atom coordinates read : 2242 total number of charged atoms : 2108 net assigned charge : 9.014021 assigned positive charge : 326.9487 centred at (gu) : 90.97509 89.37621 89.27663 assigned negative charge : -317.9353 centred at (gu) : 90.94754 89.48393 89.24686 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6347 nv = 96 ne = 84 npr = 44569 no. pairs analyzed = 44569 no. exposed pairs = 2959 no. arc points = 21540 no. surface atoms = 998 nbur = 1244 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 386 mr = 3290 m= 3 mr = 32 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 0.3300000 number of dielectric boundary points 3414 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2118 ## 163 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7475 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1204591E-08 1.2968962E-08 midg,1,midg; midg,igrid,midg 2.5189992E-08 2.2372708E-09 1,midg,midg; igrid,midg,midg 8.0969933E-09 1.8259843E-08 gauss-seidel spectral radius is 0.9872614 estimated iterations to convergence 72 setup time was (sec) 0.5900000 now iterating at: 14:31:33 rms-change max change #iterations 0.1324183 20.12590 at 10iterations 1.2910729E-02 2.289057 at 20iterations 1.2651044E-03 0.2099934 at 30iterations 1.3084439E-04 2.0280838E-02 at 40iterations 1.5656900E-05 2.3555756E-03 at 50iterations finished qdiffx linear iterations at : 14:31:44 total time elapsed so far: 3.760000 # loops : 50 mean,max change (kT/e) : 1.5656900E-05 2.3555756E-03 energy calculations done at 3.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.000000 DelPhi exited at 14:31:47 4.003u 0.162s 0:18.19 22.8% 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 Sun Oct 16 2011 at 14:31:49 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 = 2242 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 1.914665 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): -0.1830000 53.16400 ymin,ymax (A): -16.48900 27.53400 zmin,zma (A): 28.60200 84.38200 x,y,z range (A): 53.34700 44.02300 55.78000 scale (grids/A): 1.914665 object centre (A): 26.49050 5.522500 56.49200 number of atom coordinates read : 2242 total number of charged atoms : 2108 net assigned charge : 9.014021 assigned positive charge : 326.9487 centred at (gu) : 92.92521 88.12853 87.82978 assigned negative charge : -317.9353 centred at (gu) : 92.84300 88.45183 87.74068 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 68031 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21540 grid for indexing accessible points = 1.400000 m= 23997 mr = 45314 m= 3881 mr = 17012 m= 278 mr = 2286 m= 2 mr = 87 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 31490 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 118 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 16588 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) : 0.6382216 object centre at (A) : 26.49050 5.522500 56.49200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7523952E-02 4.3982696E-02 midg,1,midg; midg,igrid,midg 2.4805224E-02 -6.5006041E-03 1,midg,midg; igrid,midg,midg 3.5921760E-02 4.2835545E-02 gauss-seidel spectral radius is 0.9986254 estimated iterations to convergence 214 setup time was (sec) 0.9700000 now iterating at: 14:31:55 rms-change max change #iterations 3.855254 189.8101 at 10iterations 1.794041 65.56487 at 20iterations 0.8387248 31.08536 at 30iterations 0.3893563 13.28246 at 40iterations 0.1820770 5.963640 at 50iterations 8.4656492E-02 2.900768 at 60iterations 3.9537676E-02 1.348932 at 70iterations 1.8414592E-02 0.5590897 at 80iterations 8.5941032E-03 0.2730217 at 90iterations 4.0035951E-03 0.1329231 at 100iterations 1.8751973E-03 6.3659668E-02 at 110iterations 8.7134162E-04 2.8442383E-02 at 120iterations finished qdiffx linear iterations at : 14:32:18 total time elapsed so far: 8.630000 # loops : 120 mean,max change (kT/e) : 8.7134162E-04 2.8442383E-02 energy calculations done at 8.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.850000 DelPhi exited at 14:32:23 8.857u 0.164s 0:34.14 26.3% 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 Sun Oct 16 2011 at 14:32:27 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2242 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 2.871997 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): -0.1830000 53.16400 ymin,ymax (A): -16.48900 27.53400 zmin,zma (A): 28.60200 84.38200 x,y,z range (A): 53.34700 44.02300 55.78000 scale (grids/A): 2.871997 object centre (A): 26.49050 5.522500 56.49200 number of atom coordinates read : 2242 total number of charged atoms : 2108 net assigned charge : 9.014021 assigned positive charge : 326.9487 centred at (gu) : 94.38767 87.19272 86.74467 assigned negative charge : -317.9353 centred at (gu) : 94.26447 87.67783 86.61098 start vw surface at 0.1600000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 157003 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21540 grid for indexing accessible points = 1.400000 m= 77378 mr = 110103 m= 27902 mr = 61789 m= 6943 mr = 21781 m= 1130 mr = 4937 m= 73 mr = 722 m= 2 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.9399999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.580000 number of dielectric boundary points 71074 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.750000 number of grid points assigned charge 16863 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) : 1.914665 object centre at (A) : 26.49050 5.522500 56.49200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3396595 0.6654376 midg,1,midg; midg,igrid,midg 0.2478378 -6.4473592E-02 1,midg,midg; igrid,midg,midg 0.3822227 0.3997708 gauss-seidel spectral radius is 0.9992589 estimated iterations to convergence 290 setup time was (sec) 1.950000 now iterating at: 14:32:37 rms-change max change #iterations 9.245330 411.9911 at 10iterations 5.425076 146.6162 at 20iterations 3.153603 78.89716 at 30iterations 1.826786 38.15587 at 40iterations 1.059361 21.60572 at 50iterations 0.6105692 13.47794 at 60iterations 0.3523220 6.859268 at 70iterations 0.2026783 3.892693 at 80iterations 0.1165943 2.209327 at 90iterations 6.7048401E-02 1.393014 at 100iterations 3.8551357E-02 0.7298870 at 110iterations 2.2128521E-02 0.4293137 at 120iterations 1.2740415E-02 0.2558308 at 130iterations 7.3104198E-03 0.1361005 at 140iterations 4.1958597E-03 7.9894543E-02 at 150iterations 2.4094344E-03 4.6428680E-02 at 160iterations 1.3821359E-03 2.6016235E-02 at 170iterations 7.9558644E-04 1.4236450E-02 at 180iterations finished qdiffx linear iterations at : 14:33:10 total time elapsed so far: 14.80000 # loops : 180 mean,max change (kT/e) : 7.9558644E-04 1.4236450E-02 energy calculations done at 14.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.03000 DelPhi exited at 14:33:12 15.036u 0.235s 0:44.88 34.0% 0+0k 0+0io 0pf+0w