Sat Oct 8 12:35:33 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 8 2011 at 12:35:33 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 = 2327 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6044655 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): -18.12800 23.22900 ymin,ymax (A): -15.99700 32.48900 zmin,zma (A): 18.22900 77.12400 x,y,z range (A): 41.35700 48.48600 58.89500 scale (grids/A): 0.6044655 object centre (A): 2.550500 8.246001 47.67650 number of atom coordinates read : 2327 total number of charged atoms : 2193 net assigned charge : 2.000007 assigned positive charge : 313.9017 centred at (gu) : 89.77329 88.97313 88.82716 assigned negative charge : -311.9023 centred at (gu) : 89.71577 89.05069 89.08790 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5697 nv = 96 ne = 84 npr = 49440 no. pairs analyzed = 49440 no. exposed pairs = 3137 no. arc points = 21893 no. surface atoms = 1076 nbur = 1251 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 295 mr = 2753 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.1900000 number of dielectric boundary points 3225 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2131 ## 165 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 6993 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2260715E-08 -6.2354797E-09 midg,1,midg; midg,igrid,midg 4.3510626E-09 -1.3885224E-09 1,midg,midg; igrid,midg,midg -1.1445928E-09 2.6423925E-09 gauss-seidel spectral radius is 0.9858206 estimated iterations to convergence 69 setup time was (sec) 0.4100000 now iterating at: 12:35:34 rms-change max change #iterations 9.5154122E-02 16.34594 at 10iterations 9.5145693E-03 1.781082 at 20iterations 2.0127115E-03 0.4087868 at 30iterations 7.4967195E-04 0.1566505 at 40iterations 2.9696923E-04 6.1973572E-02 at 50iterations finished qdiffx linear iterations at : 12:35:37 total time elapsed so far: 3.550000 # loops : 50 mean,max change (kT/e) : 2.9696923E-04 6.1973572E-02 energy calculations done at 3.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.700000 DelPhi exited at 12:35:37 3.702u 0.196s 0:04.23 91.9% 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 Sat Oct 8 2011 at 12:35:37 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 = 2327 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.813397 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): -18.12800 23.22900 ymin,ymax (A): -15.99700 32.48900 zmin,zma (A): 18.22900 77.12400 x,y,z range (A): 41.35700 48.48600 58.89500 scale (grids/A): 1.813397 object centre (A): 2.550500 8.246001 47.67650 number of atom coordinates read : 2327 total number of charged atoms : 2193 net assigned charge : 2.000007 assigned positive charge : 313.9017 centred at (gu) : 89.31960 86.91930 86.48125 assigned negative charge : -311.9023 centred at (gu) : 89.14765 87.15216 87.26384 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 61714 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21893 grid for indexing accessible points = 1.400000 m= 20203 mr = 40102 m= 2960 mr = 13584 m= 128 mr = 1604 m= 2 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 567 time to turn everything in is 0.3300000 number of dielectric boundary points 29687 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 128 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 17193 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) : 0.6044655 object centre at (A) : 2.550500 8.246001 47.67650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1393960E-02 -2.0121217E-02 midg,1,midg; midg,igrid,midg 2.8483781E-03 -1.2101284E-03 1,midg,midg; igrid,midg,midg -1.6697011E-03 6.5611298E-03 gauss-seidel spectral radius is 0.9984783 estimated iterations to convergence 203 setup time was (sec) 0.5800000 now iterating at: 12:35:38 rms-change max change #iterations 3.380919 184.1974 at 10iterations 1.511995 55.55085 at 20iterations 0.6758129 27.16708 at 30iterations 0.3032632 11.89093 at 40iterations 0.1363892 4.546877 at 50iterations 6.1725356E-02 2.126322 at 60iterations 2.7848922E-02 1.061570 at 70iterations 1.2948651E-02 0.5006638 at 80iterations 6.2918938E-03 0.2584648 at 90iterations 3.3376906E-03 0.1426201 at 100iterations 1.9851543E-03 8.9817047E-02 at 110iterations 1.3235227E-03 5.7567596E-02 at 120iterations finished qdiffx linear iterations at : 12:35:46 total time elapsed so far: 8.440000 # loops : 120 mean,max change (kT/e) : 1.3235227E-03 5.7567596E-02 energy calculations done at 8.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.580000 DelPhi exited at 12:35:47 8.581u 0.249s 0:09.11 96.8% 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 Sat Oct 8 2011 at 12:35:47 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 = 2327 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.720095 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): -18.12800 23.22900 ymin,ymax (A): -15.99700 32.48900 zmin,zma (A): 18.22900 77.12400 x,y,z range (A): 41.35700 48.48600 58.89500 scale (grids/A): 2.720095 object centre (A): 2.550500 8.246001 47.67650 number of atom coordinates read : 2327 total number of charged atoms : 2193 net assigned charge : 2.000007 assigned positive charge : 313.9017 centred at (gu) : 88.97925 85.37876 84.72182 assigned negative charge : -311.9023 centred at (gu) : 88.72153 85.72829 85.89585 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 143054 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21893 grid for indexing accessible points = 1.400000 m= 66180 mr = 98690 m= 22684 mr = 51167 m= 4906 mr = 16990 m= 532 mr = 3325 m= 24 mr = 301 m= 0 mr = 5 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 1943 time to turn everything in is 0.8000000 number of dielectric boundary points 66902 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 17541 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) : 1.813397 object centre at (A) : 2.550500 8.246001 47.67650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6366393 -0.2508014 midg,1,midg; midg,igrid,midg 1.8013358E-02 -1.0115223E-02 1,midg,midg; igrid,midg,midg -2.7093364E-02 5.8474179E-02 gauss-seidel spectral radius is 0.9992160 estimated iterations to convergence 282 setup time was (sec) 1.060000 now iterating at: 12:35:48 rms-change max change #iterations 8.240875 339.2628 at 10iterations 4.730587 168.4325 at 20iterations 2.703180 58.34650 at 30iterations 1.539536 37.70931 at 40iterations 0.8748085 19.09330 at 50iterations 0.4968887 13.30896 at 60iterations 0.2816389 6.720062 at 70iterations 0.1598122 3.257779 at 80iterations 9.0664305E-02 1.754179 at 90iterations 5.1302832E-02 1.144399 at 100iterations 2.9026059E-02 0.6461792 at 110iterations 1.6475003E-02 0.3266373 at 120iterations 9.4008800E-03 0.2199860 at 130iterations 5.4015401E-03 0.1146965 at 140iterations 3.1562427E-03 7.6953888E-02 at 150iterations 1.9083210E-03 4.2709351E-02 at 160iterations 1.2171845E-03 2.9624939E-02 at 170iterations 8.3896401E-04 2.1339417E-02 at 180iterations finished qdiffx linear iterations at : 12:36:00 total time elapsed so far: 13.25000 # loops : 180 mean,max change (kT/e) : 8.3896401E-04 2.1339417E-02 energy calculations done at 13.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.38000 DelPhi exited at 12:36:01 13.383u 0.249s 0:13.91 97.9% 0+0k 0+0io 0pf+0w