Mon Oct 10 19:39:07 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 Mon Oct 10 2011 at 19:39:07 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2923 !!! WARNING: GLM 98 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5889165 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): -4.351000 46.58900 ymin,ymax (A): -25.91800 34.53200 zmin,zma (A): -14.69100 37.85100 x,y,z range (A): 50.94000 60.45000 52.54200 scale (grids/A): 0.5889165 object centre (A): 21.11900 4.306999 11.58000 number of atom coordinates read : 2923 total number of charged atoms : 2778 net assigned charge : 1.906031 assigned positive charge : 436.1284 centred at (gu) : 90.06189 90.35317 89.76801 assigned negative charge : -434.2234 centred at (gu) : 90.10859 90.51937 89.90196 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6739 nv = 96 ne = 84 npr = 58736 no. pairs analyzed = 58736 no. exposed pairs = 3653 no. arc points = 25958 no. surface atoms = 1234 nbur = 1689 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 300 mr = 3574 m= 3 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.2200000 number of dielectric boundary points 3452 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2659 ## 281 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8519 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.6236033E-09 -3.1564849E-09 midg,1,midg; midg,igrid,midg 4.8582982E-09 -4.6727791E-09 1,midg,midg; igrid,midg,midg 1.8927566E-09 -7.8063911E-10 gauss-seidel spectral radius is 0.9851137 estimated iterations to convergence 67 setup time was (sec) 0.4100000 now iterating at: 19:39:08 rms-change max change #iterations 0.1065676 18.03792 at 10iterations 8.6324783E-03 1.253323 at 20iterations 7.0644141E-04 0.1076112 at 30iterations 5.7819139E-05 9.1333389E-03 at 40iterations 4.8394950E-06 7.0571899E-04 at 50iterations finished qdiffx linear iterations at : 19:39:11 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 4.8394950E-06 7.0571899E-04 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 19:39:11 3.411u 0.183s 0:04.08 87.9% 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 Mon Oct 10 2011 at 19:39:11 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2923 !!! WARNING: GLM 98 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.766750 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): -4.351000 46.58900 ymin,ymax (A): -25.91800 34.53200 zmin,zma (A): -14.69100 37.85100 x,y,z range (A): 50.94000 60.45000 52.54200 scale (grids/A): 1.766750 object centre (A): 21.11900 4.306999 11.58000 number of atom coordinates read : 2923 total number of charged atoms : 2778 net assigned charge : 1.906031 assigned positive charge : 436.1284 centred at (gu) : 90.18538 91.05898 89.30321 assigned negative charge : -434.2234 centred at (gu) : 90.32561 91.55773 89.70580 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 73623 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25958 grid for indexing accessible points = 1.400000 m= 24575 mr = 50198 m= 3108 mr = 17645 m= 92 mr = 1612 m= 0 mr = 2 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 1319 time to turn everything in is 0.3600000 number of dielectric boundary points 31941 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 223 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 21657 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) : 0.5889165 object centre at (A) : 21.11900 4.306999 11.58000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.7916346E-03 -2.5606042E-02 midg,1,midg; midg,igrid,midg 1.5250101E-02 -1.0377714E-02 1,midg,midg; igrid,midg,midg 3.2217745E-03 -1.6773685E-03 gauss-seidel spectral radius is 0.9984549 estimated iterations to convergence 202 setup time was (sec) 0.5800000 now iterating at: 19:39:12 rms-change max change #iterations 3.922212 165.5686 at 10iterations 1.747593 60.44842 at 20iterations 0.7759402 25.78485 at 30iterations 0.3460502 11.14674 at 40iterations 0.1545455 5.078557 at 50iterations 6.8994708E-02 2.376172 at 60iterations 3.0836955E-02 1.098976 at 70iterations 1.3743022E-02 0.5053787 at 80iterations 6.1318325E-03 0.2167025 at 90iterations 2.7381505E-03 9.3715668E-02 at 100iterations 1.2196297E-03 3.9000511E-02 at 110iterations 5.4501457E-04 1.8617868E-02 at 120iterations finished qdiffx linear iterations at : 19:39:19 total time elapsed so far: 7.670000 # loops : 120 mean,max change (kT/e) : 5.4501457E-04 1.8617868E-02 energy calculations done at 7.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.800000 DelPhi exited at 19:39:20 7.801u 0.218s 0:08.78 91.2% 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 Mon Oct 10 2011 at 19:39:20 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2923 !!! WARNING: GLM 98 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.650124 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): -4.351000 46.58900 ymin,ymax (A): -25.91800 34.53200 zmin,zma (A): -14.69100 37.85100 x,y,z range (A): 50.94000 60.45000 52.54200 scale (grids/A): 2.650124 object centre (A): 21.11900 4.306999 11.58000 number of atom coordinates read : 2923 total number of charged atoms : 2778 net assigned charge : 1.906031 assigned positive charge : 436.1284 centred at (gu) : 90.27782 91.58814 88.95460 assigned negative charge : -434.2234 centred at (gu) : 90.48833 92.33653 89.55862 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 170659 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25958 grid for indexing accessible points = 1.400000 m= 82055 mr = 122394 m= 26789 mr = 66083 m= 5279 mr = 20934 m= 499 mr = 3501 m= 13 mr = 260 m= 0 mr = 0 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 4490 time to turn everything in is 0.8900000 number of dielectric boundary points 72122 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 22214 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) : 1.766750 object centre at (A) : 21.11900 4.306999 11.58000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.7912728E-02 -0.3427562 midg,1,midg; midg,igrid,midg 0.1099102 -0.1770988 1,midg,midg; igrid,midg,midg 6.4693384E-02 -5.9245441E-02 gauss-seidel spectral radius is 0.9992193 estimated iterations to convergence 283 setup time was (sec) 1.140000 now iterating at: 19:39:21 rms-change max change #iterations 9.563516 291.1841 at 10iterations 5.541105 127.1705 at 20iterations 3.163104 65.00497 at 30iterations 1.801869 37.57615 at 40iterations 1.024111 22.20473 at 50iterations 0.5814285 11.93819 at 60iterations 0.3289646 6.450639 at 70iterations 0.1867143 3.550599 at 80iterations 0.1056573 2.048588 at 90iterations 5.9735406E-02 1.131204 at 100iterations 3.3769470E-02 0.6904259 at 110iterations 1.9080065E-02 0.3843689 at 120iterations 1.0792391E-02 0.1970816 at 130iterations 6.1060898E-03 0.1154480 at 140iterations 3.4465031E-03 6.5055847E-02 at 150iterations 1.9504065E-03 3.6170959E-02 at 160iterations 1.1017983E-03 2.1293640E-02 at 170iterations 6.2262674E-04 1.2641191E-02 at 180iterations finished qdiffx linear iterations at : 19:39:33 total time elapsed so far: 12.51000 # loops : 180 mean,max change (kT/e) : 6.2262674E-04 1.2641191E-02 energy calculations done at 12.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.63000 DelPhi exited at 19:39:33 12.637u 0.232s 0:13.15 97.7% 0+0k 0+0io 0pf+0w