Sat Oct 8 23:51:03 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 Sat Oct 8 2011 at 23:51:03 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2173 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 0.6640800 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): -26.99500 26.61300 ymin,ymax (A): -15.41400 27.88800 zmin,zma (A): -3.546000 49.39800 x,y,z range (A): 53.60800 43.30200 52.94400 scale (grids/A): 0.6640800 object centre (A): -0.1910009 6.237000 22.92600 number of atom coordinates read : 2173 total number of charged atoms : 2039 net assigned charge : 11.51402 assigned positive charge : 318.9288 centred at (gu) : 90.64514 88.88158 88.52200 assigned negative charge : -307.4152 centred at (gu) : 90.64050 88.93880 88.48989 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7087 nv = 96 ne = 84 npr = 41141 no. pairs analyzed = 41141 no. exposed pairs = 3124 no. arc points = 22507 no. surface atoms = 1025 nbur = 1148 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 501 mr = 3661 m= 1 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3847 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2106 ## 202 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7742 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.6109530E-08 2.8338000E-08 midg,1,midg; midg,igrid,midg 5.3181143E-08 1.8160200E-08 1,midg,midg; igrid,midg,midg 2.7893519E-08 3.7904666E-08 gauss-seidel spectral radius is 0.9882286 estimated iterations to convergence 75 setup time was (sec) 0.5800000 now iterating at: 23:51:04 rms-change max change #iterations 0.1541443 23.28898 at 10iterations 1.6605962E-02 2.270416 at 20iterations 1.7756625E-03 0.2690372 at 30iterations 1.9477333E-04 2.6988506E-02 at 40iterations 2.2465943E-05 3.1223297E-03 at 50iterations finished qdiffx linear iterations at : 23:51:08 total time elapsed so far: 4.510000 # loops : 50 mean,max change (kT/e) : 2.2465943E-05 3.1223297E-03 energy calculations done at 4.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.690000 DelPhi exited at 23:51:08 4.698u 0.358s 0:05.37 93.8% 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 23:51:09 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2173 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 1.992240 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): -26.99500 26.61300 ymin,ymax (A): -15.41400 27.88800 zmin,zma (A): -3.546000 49.39800 x,y,z range (A): 53.60800 43.30200 52.94400 scale (grids/A): 1.992240 object centre (A): -0.1910009 6.237000 22.92600 number of atom coordinates read : 2173 total number of charged atoms : 2039 net assigned charge : 11.51402 assigned positive charge : 318.9288 centred at (gu) : 91.93520 86.64468 85.56573 assigned negative charge : -307.4152 centred at (gu) : 91.92182 86.81638 85.46983 start vw surface at 0.1100000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 74244 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22507 grid for indexing accessible points = 1.400000 m= 29942 mr = 48999 m= 6144 mr = 21947 m= 517 mr = 3974 m= 5 mr = 248 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 35684 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 130 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 16095 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) : 0.6640800 object centre at (A) : -0.1910009 6.237000 22.92600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2747012E-02 6.0434815E-02 midg,1,midg; midg,igrid,midg 2.9004777E-02 -1.5448254E-03 1,midg,midg; igrid,midg,midg 5.5767816E-02 6.1240576E-02 gauss-seidel spectral radius is 0.9987285 estimated iterations to convergence 222 setup time was (sec) 0.9100000 now iterating at: 23:51:10 rms-change max change #iterations 4.132089 193.5621 at 10iterations 1.971097 67.98070 at 20iterations 0.9470405 29.95613 at 30iterations 0.4530331 16.61420 at 40iterations 0.2165831 6.796707 at 50iterations 0.1044621 3.606632 at 60iterations 4.9995057E-02 1.557964 at 70iterations 2.4075339E-02 0.7657375 at 80iterations 1.1579118E-02 0.3712170 at 90iterations 5.5516679E-03 0.1777344 at 100iterations 2.6708301E-03 7.5151622E-02 at 110iterations 1.2783479E-03 4.0365219E-02 at 120iterations finished qdiffx linear iterations at : 23:51:20 total time elapsed so far: 10.61000 # loops : 120 mean,max change (kT/e) : 1.2783479E-03 4.0365219E-02 energy calculations done at 10.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.77000 DelPhi exited at 23:51:20 10.779u 0.434s 0:11.55 96.9% 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 23:51:20 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2173 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 2.988360 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): -26.99500 26.61300 ymin,ymax (A): -15.41400 27.88800 zmin,zma (A): -3.546000 49.39800 x,y,z range (A): 53.60800 43.30200 52.94400 scale (grids/A): 2.988360 object centre (A): -0.1910009 6.237000 22.92600 number of atom coordinates read : 2173 total number of charged atoms : 2039 net assigned charge : 11.51402 assigned positive charge : 318.9288 centred at (gu) : 92.90278 84.96693 83.34883 assigned negative charge : -307.4152 centred at (gu) : 92.88274 85.22474 83.20480 start vw surface at 0.1100000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 170837 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22507 grid for indexing accessible points = 1.400000 m= 91221 mr = 118763 m= 38851 mr = 73898 m= 11511 mr = 31287 m= 2219 mr = 8705 m= 205 mr = 1588 m= 3 mr = 125 m= 0 mr = 0 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.660000 number of dielectric boundary points 80481 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.790000 number of grid points assigned charge 16304 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) : 1.992240 object centre at (A) : -0.1910009 6.237000 22.92600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3464350 0.8469529 midg,1,midg; midg,igrid,midg 0.2212618 -1.8716911E-02 1,midg,midg; igrid,midg,midg 0.5755664 0.5095584 gauss-seidel spectral radius is 0.9992968 estimated iterations to convergence 298 setup time was (sec) 1.990000 now iterating at: 23:51:23 rms-change max change #iterations 9.734745 419.7968 at 10iterations 5.824479 147.1458 at 20iterations 3.466590 83.66331 at 30iterations 2.053858 44.80626 at 40iterations 1.212385 26.09778 at 50iterations 0.7133961 14.41449 at 60iterations 0.4192237 9.499526 at 70iterations 0.2464875 4.919178 at 80iterations 0.1441845 3.172022 at 90iterations 8.4212705E-02 1.630538 at 100iterations 4.9313955E-02 0.9921989 at 110iterations 2.8788485E-02 0.5975380 at 120iterations 1.6769236E-02 0.3085046 at 130iterations 9.7948425E-03 0.1805248 at 140iterations 5.7059950E-03 0.1063557 at 150iterations 3.3360063E-03 6.4526081E-02 at 160iterations 1.9434578E-03 3.2886505E-02 at 170iterations 1.1348813E-03 2.1606445E-02 at 180iterations finished qdiffx linear iterations at : 23:51:39 total time elapsed so far: 18.94000 # loops : 180 mean,max change (kT/e) : 1.1348813E-03 2.1606445E-02 energy calculations done at 18.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.10000 DelPhi exited at 23:51:40 19.101u 0.479s 0:19.83 98.6% 0+0k 0+0io 0pf+0w