Mon Oct 10 19:32:05 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 Mon Oct 10 2011 at 19:32:05 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 = 2560 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: 0.5656091 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): 40.30500 94.18200 ymin,ymax (A): -72.13200 -9.191000 zmin,zma (A): 66.79700 112.3880 x,y,z range (A): 53.87700 62.94099 45.59100 scale (grids/A): 0.5656091 object centre (A): 67.24350 -40.66150 89.59250 number of atom coordinates read : 2560 total number of charged atoms : 2420 net assigned charge : 0.5000076 assigned positive charge : 389.1085 centred at (gu) : 90.08900 91.88457 90.58006 assigned negative charge : -388.6094 centred at (gu) : 90.12141 91.79398 90.72891 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5377 nv = 96 ne = 84 npr = 50961 no. pairs analyzed = 50961 no. exposed pairs = 3270 no. arc points = 22716 no. surface atoms = 1094 nbur = 1466 mkacc time = 0.1100000 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 = 1.512000 m= 217 mr = 2835 m= 0 mr = 16 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 2743 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2420 ## 316 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 6961 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5415653E-09 -1.9891087E-09 midg,1,midg; midg,igrid,midg -6.4644923E-10 1.7632190E-09 1,midg,midg; igrid,midg,midg 4.2641643E-10 -3.3328681E-10 gauss-seidel spectral radius is 0.9838376 estimated iterations to convergence 65 setup time was (sec) 0.5000000 now iterating at: 19:32:06 rms-change max change #iterations 8.0305807E-02 13.05655 at 10iterations 6.4167995E-03 1.013794 at 20iterations 7.6690223E-04 0.1519737 at 30iterations 1.6074018E-04 3.2803535E-02 at 40iterations 4.0186886E-05 8.2826614E-03 at 50iterations finished qdiffx linear iterations at : 19:32:08 total time elapsed so far: 2.920000 # loops : 50 mean,max change (kT/e) : 4.0186886E-05 8.2826614E-03 energy calculations done at 2.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.080000 DelPhi exited at 19:32:09 3.086u 0.141s 0:04.16 77.4% 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 Mon Oct 10 2011 at 19:32:10 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 = 2560 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: 1.696827 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): 40.30500 94.18200 ymin,ymax (A): -72.13200 -9.191000 zmin,zma (A): 66.79700 112.3880 x,y,z range (A): 53.87700 62.94099 45.59100 scale (grids/A): 1.696827 object centre (A): 67.24350 -40.66150 89.59250 number of atom coordinates read : 2560 total number of charged atoms : 2420 net assigned charge : 0.5000076 assigned positive charge : 389.1085 centred at (gu) : 90.26649 95.65298 91.73927 assigned negative charge : -388.6094 centred at (gu) : 90.36393 95.38168 92.18650 start vw surface at 0.1400000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 59266 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22716 grid for indexing accessible points = 1.400000 m= 19590 mr = 40637 m= 2195 mr = 13979 m= 71 mr = 1160 m= 0 mr = 13 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 463 time to turn everything in is 0.4200000 number of dielectric boundary points 25333 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 278 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 18696 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) : 0.5656091 object centre at (A) : 67.24350 -40.66150 89.59250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.7546371E-03 -7.2371596E-03 midg,1,midg; midg,igrid,midg -1.0746997E-02 1.5029822E-02 1,midg,midg; igrid,midg,midg 1.5704907E-02 -4.4957367E-03 gauss-seidel spectral radius is 0.9982760 estimated iterations to convergence 191 setup time was (sec) 0.6700000 now iterating at: 19:32:10 rms-change max change #iterations 3.345623 190.9712 at 10iterations 1.416822 58.43291 at 20iterations 0.6041800 23.83833 at 30iterations 0.2578691 9.940670 at 40iterations 0.1101735 4.273546 at 50iterations 4.7027055E-02 1.705719 at 60iterations 2.0131089E-02 0.8008776 at 70iterations 8.7032514E-03 0.3225329 at 80iterations 3.8187469E-03 0.1431961 at 90iterations 1.7277225E-03 7.0713043E-02 at 100iterations 8.2465477E-04 3.2554626E-02 at 110iterations 4.2541645E-04 1.7692566E-02 at 120iterations finished qdiffx linear iterations at : 19:32:16 total time elapsed so far: 6.550000 # loops : 120 mean,max change (kT/e) : 4.2541645E-04 1.7692566E-02 energy calculations done at 6.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.720000 DelPhi exited at 19:32:17 6.726u 0.177s 0:07.64 90.1% 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 19:32:17 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 = 2560 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: 2.545241 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): 40.30500 94.18200 ymin,ymax (A): -72.13200 -9.191000 zmin,zma (A): 66.79700 112.3880 x,y,z range (A): 53.87700 62.94099 45.59100 scale (grids/A): 2.545241 object centre (A): 67.24350 -40.66150 89.59250 number of atom coordinates read : 2560 total number of charged atoms : 2420 net assigned charge : 0.5000076 assigned positive charge : 389.1085 centred at (gu) : 90.39951 98.47928 92.60883 assigned negative charge : -388.6094 centred at (gu) : 90.54580 98.07253 93.27972 start vw surface at 0.1600000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 137538 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22716 grid for indexing accessible points = 1.400000 m= 65832 mr = 99123 m= 20742 mr = 53042 m= 3732 mr = 16026 m= 291 mr = 2544 m= 6 mr = 133 m= 0 mr = 0 time to grow re-entrant surface = 0.5600000 no. cavity mid-points inaccessible to solvent = 1414 time to turn everything in is 1.010000 number of dielectric boundary points 57273 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 19341 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) : 1.696827 object centre at (A) : 67.24350 -40.66150 89.59250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.2251400E-02 -6.8515129E-02 midg,1,midg; midg,igrid,midg -8.0020025E-02 0.4546323 1,midg,midg; igrid,midg,midg 0.2960358 -0.1272053 gauss-seidel spectral radius is 0.9991531 estimated iterations to convergence 271 setup time was (sec) 1.290000 now iterating at: 19:32:19 rms-change max change #iterations 8.438980 270.4568 at 10iterations 4.737508 126.6738 at 20iterations 2.651313 79.17766 at 30iterations 1.482279 34.58551 at 40iterations 0.8230760 19.01576 at 50iterations 0.4576282 10.29478 at 60iterations 0.2538819 5.513586 at 70iterations 0.1406731 3.009403 at 80iterations 7.7750154E-02 1.641530 at 90iterations 4.3090217E-02 0.9155674 at 100iterations 2.3905260E-02 0.5121422 at 110iterations 1.3207665E-02 0.2856569 at 120iterations 7.3046368E-03 0.1496353 at 130iterations 4.0624137E-03 8.8563919E-02 at 140iterations 2.2586600E-03 4.8009872E-02 at 150iterations 1.2673191E-03 2.7934074E-02 at 160iterations 7.1899605E-04 1.5092850E-02 at 170iterations 4.1802108E-04 9.9029541E-03 at 180iterations finished qdiffx linear iterations at : 19:32:28 total time elapsed so far: 10.84000 # loops : 180 mean,max change (kT/e) : 4.1802108E-04 9.9029541E-03 energy calculations done at 10.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.01000 DelPhi exited at 19:32:29 11.015u 0.191s 0:11.72 95.5% 0+0k 0+0io 0pf+0w