Tue Oct 11 08:34:41 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 Tue Oct 11 2011 at 08:34:41 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2705 !!! WARNING: GLM 262 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6599926 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): -8.665999 45.27400 ymin,ymax (A): -15.90400 31.24800 zmin,zma (A): -10.28400 43.19100 x,y,z range (A): 53.94000 47.15200 53.47500 scale (grids/A): 0.6599926 object centre (A): 18.30400 7.672001 16.45350 number of atom coordinates read : 2705 total number of charged atoms : 2557 net assigned charge : 4.406013 assigned positive charge : 410.3227 centred at (gu) : 89.65835 89.80083 89.22201 assigned negative charge : -405.9172 centred at (gu) : 89.80181 89.69312 89.25796 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7971 nv = 96 ne = 84 npr = 54532 no. pairs analyzed = 54532 no. exposed pairs = 3247 no. arc points = 22468 no. surface atoms = 1098 nbur = 1607 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 472 mr = 4547 m= 0 mr = 84 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 131 time to turn everything in is 0.3100000 number of dielectric boundary points 3812 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2095 ## 181 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 9245 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1733838E-08 3.1729475E-09 midg,1,midg; midg,igrid,midg -1.1962646E-08 3.1789376E-08 1,midg,midg; igrid,midg,midg 4.3326899E-08 -1.7660163E-08 gauss-seidel spectral radius is 0.9881103 estimated iterations to convergence 75 setup time was (sec) 0.5200000 now iterating at: 08:34:42 rms-change max change #iterations 0.1778573 26.20393 at 10iterations 1.9350663E-02 2.508522 at 20iterations 2.7308678E-03 0.5051613 at 30iterations 6.7643379E-04 0.1434860 at 40iterations 2.2611549E-04 4.9030304E-02 at 50iterations finished qdiffx linear iterations at : 08:34:44 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 2.2611549E-04 4.9030304E-02 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.130000 DelPhi exited at 08:34:45 3.136u 0.143s 0:03.65 89.5% 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 Tue Oct 11 2011 at 08:34:45 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2705 !!! WARNING: GLM 262 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.979978 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): -8.665999 45.27400 ymin,ymax (A): -15.90400 31.24800 zmin,zma (A): -10.28400 43.19100 x,y,z range (A): 53.94000 47.15200 53.47500 scale (grids/A): 1.979978 object centre (A): 18.30400 7.672001 16.45350 number of atom coordinates read : 2705 total number of charged atoms : 2557 net assigned charge : 4.406013 assigned positive charge : 410.3227 centred at (gu) : 88.97436 89.40179 87.66515 assigned negative charge : -405.9172 centred at (gu) : 89.40525 89.07907 87.77341 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 86000 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22468 grid for indexing accessible points = 1.400000 m= 32333 mr = 60790 m= 5666 mr = 24500 m= 393 mr = 3831 m= 4 mr = 162 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 4972 time to turn everything in is 0.5900000 number of dielectric boundary points 35113 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 119 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 20207 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) : 0.6599926 object centre at (A) : 18.30400 7.672001 16.45350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4307545E-02 5.7844990E-03 midg,1,midg; midg,igrid,midg 1.3826291E-02 2.1330470E-02 1,midg,midg; igrid,midg,midg 5.8739051E-02 -3.3920757E-02 gauss-seidel spectral radius is 0.9987400 estimated iterations to convergence 223 setup time was (sec) 0.8500000 now iterating at: 08:34:46 rms-change max change #iterations 4.719346 179.3024 at 10iterations 2.282290 71.27477 at 20iterations 1.099057 33.61489 at 30iterations 0.5297385 15.42527 at 40iterations 0.2557095 7.676182 at 50iterations 0.1234700 3.774784 at 60iterations 5.9770759E-02 1.769707 at 70iterations 2.8995465E-02 0.8233261 at 80iterations 1.4217317E-02 0.4206113 at 90iterations 6.9920090E-03 0.2059965 at 100iterations 3.5170892E-03 0.1124496 at 110iterations 1.8539897E-03 6.3109398E-02 at 120iterations finished qdiffx linear iterations at : 08:34:52 total time elapsed so far: 7.000000 # loops : 120 mean,max change (kT/e) : 1.8539897E-03 6.3109398E-02 energy calculations done at 7.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.170000 DelPhi exited at 08:34:53 7.168u 0.164s 0:07.75 94.4% 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 Tue Oct 11 2011 at 08:34:53 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2705 !!! WARNING: GLM 262 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.969967 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): -8.665999 45.27400 ymin,ymax (A): -15.90400 31.24800 zmin,zma (A): -10.28400 43.19100 x,y,z range (A): 53.94000 47.15200 53.47500 scale (grids/A): 2.969967 object centre (A): 18.30400 7.672001 16.45350 number of atom coordinates read : 2705 total number of charged atoms : 2557 net assigned charge : 4.406013 assigned positive charge : 410.3227 centred at (gu) : 88.46140 89.10256 86.49765 assigned negative charge : -405.9172 centred at (gu) : 89.10783 88.61846 86.66007 start vw surface at 0.1200000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 198553 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22468 grid for indexing accessible points = 1.400000 m= 103498 mr = 146564 m= 39529 mr = 86169 m= 10606 mr = 32523 m= 1767 mr = 8341 m= 102 mr = 1278 m= 1 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.8799999 no. cavity mid-points inaccessible to solvent = 17486 time to turn everything in is 1.450000 number of dielectric boundary points 79147 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.570000 number of grid points assigned charge 20455 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) : 1.979978 object centre at (A) : 18.30400 7.672001 16.45350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3008286 -0.1140887 midg,1,midg; midg,igrid,midg 0.2859288 0.1935294 1,midg,midg; igrid,midg,midg 0.8138569 -0.4547557 gauss-seidel spectral radius is 0.9992790 estimated iterations to convergence 294 setup time was (sec) 1.720000 now iterating at: 08:34:55 rms-change max change #iterations 10.81231 390.8185 at 10iterations 6.305239 126.0256 at 20iterations 3.675432 79.54848 at 30iterations 2.133913 36.87546 at 40iterations 1.239193 22.45677 at 50iterations 0.7196870 13.32541 at 60iterations 0.4178962 7.376124 at 70iterations 0.2419186 4.004326 at 80iterations 0.1404564 2.374146 at 90iterations 8.1243895E-02 1.486506 at 100iterations 4.7157697E-02 0.8192749 at 110iterations 2.7362367E-02 0.4761872 at 120iterations 1.5930487E-02 0.2764549 at 130iterations 9.3418006E-03 0.1757393 at 140iterations 5.5549988E-03 0.1033363 at 150iterations 3.3608677E-03 8.3103180E-02 at 160iterations 2.1000116E-03 4.6371460E-02 at 170iterations 1.3887909E-03 3.1150818E-02 at 180iterations finished qdiffx linear iterations at : 08:35:04 total time elapsed so far: 11.15000 # loops : 180 mean,max change (kT/e) : 1.3887909E-03 3.1150818E-02 energy calculations done at 11.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.32000 DelPhi exited at 08:35:05 11.322u 0.187s 0:11.92 96.4% 0+0k 0+0io 0pf+0w