Tue Oct 11 05:27:01 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 Tue Oct 11 2011 at 05:27:01 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 = 2008 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: 0.7506748 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): -2.779000 44.64500 ymin,ymax (A): -22.07100 24.41500 zmin,zma (A): 5.525000 48.30300 x,y,z range (A): 47.42400 46.48600 42.77800 scale (grids/A): 0.7506748 object centre (A): 20.93300 1.172000 26.91400 number of atom coordinates read : 2008 total number of charged atoms : 1880 net assigned charge : 6.500006 assigned positive charge : 302.9601 centred at (gu) : 90.39417 88.89272 89.86826 assigned negative charge : -296.4602 centred at (gu) : 90.30225 89.03120 89.75507 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7956 nv = 96 ne = 84 npr = 39950 no. pairs analyzed = 39950 no. exposed pairs = 2433 no. arc points = 16814 no. surface atoms = 827 nbur = 1181 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 589 mr = 4669 m= 6 mr = 135 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3747 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1470 ## 142 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8127 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.3697227E-09 2.6577877E-07 midg,1,midg; midg,igrid,midg 3.6955424E-07 -1.6136052E-08 1,midg,midg; igrid,midg,midg 3.1885431E-08 2.6651182E-07 gauss-seidel spectral radius is 0.9907365 estimated iterations to convergence 84 setup time was (sec) 0.4900000 now iterating at: 05:27:02 rms-change max change #iterations 0.2518927 37.43052 at 10iterations 3.5477120E-02 4.968319 at 20iterations 5.0409669E-03 0.6456413 at 30iterations 7.8967673E-04 9.8861694E-02 at 40iterations 1.6608210E-04 1.7002106E-02 at 50iterations finished qdiffx linear iterations at : 05:27:05 total time elapsed so far: 3.070000 # loops : 50 mean,max change (kT/e) : 1.6608210E-04 1.7002106E-02 energy calculations done at 3.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.240000 DelPhi exited at 05:27:05 3.246u 0.202s 0:04.01 85.7% 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 05:27:05 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 = 2008 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: 2.252024 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): -2.779000 44.64500 ymin,ymax (A): -22.07100 24.41500 zmin,zma (A): 5.525000 48.30300 x,y,z range (A): 47.42400 46.48600 42.77800 scale (grids/A): 2.252024 object centre (A): 20.93300 1.172000 26.91400 number of atom coordinates read : 2008 total number of charged atoms : 1880 net assigned charge : 6.500006 assigned positive charge : 302.9601 centred at (gu) : 91.18247 86.67828 89.60484 assigned negative charge : -296.4602 centred at (gu) : 90.90688 87.09354 89.26538 start vw surface at 0.1800000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 83393 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16814 grid for indexing accessible points = 1.400000 m= 36324 mr = 59977 m= 8116 mr = 28399 m= 921 mr = 5683 m= 40 mr = 521 m= 0 mr = 12 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6900000 number of dielectric boundary points 34202 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 44 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 14990 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) : 0.7506748 object centre at (A) : 20.93300 1.172000 26.91400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9339668E-02 3.8365874E-02 midg,1,midg; midg,igrid,midg 4.9869280E-02 -5.8836557E-02 1,midg,midg; igrid,midg,midg 7.8199178E-02 0.1037423 gauss-seidel spectral radius is 0.9989393 estimated iterations to convergence 243 setup time was (sec) 0.9600000 now iterating at: 05:27:07 rms-change max change #iterations 4.964557 172.2450 at 10iterations 2.552772 87.94297 at 20iterations 1.307453 45.17405 at 30iterations 0.6736310 20.67549 at 40iterations 0.3465161 9.805174 at 50iterations 0.1776016 4.598085 at 60iterations 9.1289267E-02 2.431774 at 70iterations 4.6746075E-02 1.291238 at 80iterations 2.4079261E-02 0.6672249 at 90iterations 1.2484324E-02 0.3543091 at 100iterations 6.4716712E-03 0.1867142 at 110iterations 3.4021435E-03 9.5489502E-02 at 120iterations finished qdiffx linear iterations at : 05:27:13 total time elapsed so far: 7.540000 # loops : 120 mean,max change (kT/e) : 3.4021435E-03 9.5489502E-02 energy calculations done at 7.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.720000 DelPhi exited at 05:27:14 7.720u 0.235s 0:08.49 93.6% 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 Tue Oct 11 2011 at 05:27:14 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 = 2008 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: 3.378036 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): -2.779000 44.64500 ymin,ymax (A): -22.07100 24.41500 zmin,zma (A): 5.525000 48.30300 x,y,z range (A): 47.42400 46.48600 42.77800 scale (grids/A): 3.378036 object centre (A): 20.93300 1.172000 26.91400 number of atom coordinates read : 2008 total number of charged atoms : 1880 net assigned charge : 6.500006 assigned positive charge : 302.9601 centred at (gu) : 91.77393 85.01753 89.40732 assigned negative charge : -296.4602 centred at (gu) : 91.36038 85.64037 88.89799 start vw surface at 0.1600000 fill in re-entrant regions at 0.8900000 boundary points on vw surface= 191808 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16814 grid for indexing accessible points = 1.400000 m= 109570 mr = 143696 m= 49145 mr = 92660 m= 15889 mr = 41380 m= 3665 mr = 12605 m= 561 mr = 2751 m= 40 mr = 394 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.050000 number of dielectric boundary points 77175 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.200000 number of grid points assigned charge 15040 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) : 2.252024 object centre at (A) : 20.93300 1.172000 26.91400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1785118 0.2172359 midg,1,midg; midg,igrid,midg 0.4791147 -0.5922968 1,midg,midg; igrid,midg,midg 0.5412586 0.7114278 gauss-seidel spectral radius is 0.9993255 estimated iterations to convergence 304 setup time was (sec) 2.370000 now iterating at: 05:27:17 rms-change max change #iterations 10.77129 253.7776 at 10iterations 6.482665 136.3377 at 20iterations 3.876354 67.97876 at 30iterations 2.313113 43.30397 at 40iterations 1.378041 24.87280 at 50iterations 0.8188826 13.33658 at 60iterations 0.4866714 9.077243 at 70iterations 0.2889195 4.812389 at 80iterations 0.1714926 2.883664 at 90iterations 0.1018079 1.633781 at 100iterations 6.0402129E-02 1.100472 at 110iterations 3.5952881E-02 0.6341438 at 120iterations 2.1585140E-02 0.3573265 at 130iterations 1.3096844E-02 0.2317271 at 140iterations 8.1357732E-03 0.1354675 at 150iterations 5.2511836E-03 9.2937469E-02 at 160iterations 3.5592550E-03 7.0751190E-02 at 170iterations 2.5667667E-03 4.5806885E-02 at 180iterations finished qdiffx linear iterations at : 05:27:27 total time elapsed so far: 12.85000 # loops : 180 mean,max change (kT/e) : 2.5667667E-03 4.5806885E-02 energy calculations done at 12.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.05000 DelPhi exited at 05:27:28 13.052u 0.219s 0:13.89 95.4% 0+0k 0+0io 0pf+0w