Sat Oct 8 14:38:24 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 14:38:24 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3001 !!! WARNING: NDP 318 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6401956 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): -12.07000 43.53800 ymin,ymax (A): -22.78600 22.64800 zmin,zma (A): -6.399000 47.62000 x,y,z range (A): 55.60800 45.43400 54.01900 scale (grids/A): 0.6401956 object centre (A): 15.73400 -6.9000244E-02 20.61050 number of atom coordinates read : 3001 total number of charged atoms : 2856 net assigned charge : 1.000008 assigned positive charge : 449.2226 centred at (gu) : 88.77739 89.66464 91.36164 assigned negative charge : -448.2233 centred at (gu) : 88.70139 89.51227 91.38074 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8125 nv = 96 ne = 84 npr = 63077 no. pairs analyzed = 63077 no. exposed pairs = 3341 no. arc points = 23674 no. surface atoms = 1143 nbur = 1858 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 391 mr = 4761 m= 3 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.3300000 number of dielectric boundary points 3711 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2271 ## 184 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9917 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.2266081E-09 -1.1704109E-09 midg,1,midg; midg,igrid,midg -2.0630488E-08 2.0416635E-08 1,midg,midg; igrid,midg,midg -1.1283658E-08 9.1537444E-09 gauss-seidel spectral radius is 0.9873884 estimated iterations to convergence 73 setup time was (sec) 0.5600000 now iterating at: 14:38:25 rms-change max change #iterations 0.1566565 22.01899 at 10iterations 1.5652863E-02 2.047496 at 20iterations 1.5844906E-03 0.2159643 at 30iterations 1.6478325E-04 2.0738602E-02 at 40iterations 1.8598446E-05 3.0746460E-03 at 50iterations finished qdiffx linear iterations at : 14:38:28 total time elapsed so far: 3.060000 # loops : 50 mean,max change (kT/e) : 1.8598446E-05 3.0746460E-03 energy calculations done at 3.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.240000 DelPhi exited at 14:38:28 3.241u 0.149s 0:03.72 90.8% 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 14:38:28 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3001 !!! WARNING: NDP 318 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.920587 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): -12.07000 43.53800 ymin,ymax (A): -22.78600 22.64800 zmin,zma (A): -6.399000 47.62000 x,y,z range (A): 55.60800 45.43400 54.01900 scale (grids/A): 1.920587 object centre (A): 15.73400 -6.9000244E-02 20.61050 number of atom coordinates read : 3001 total number of charged atoms : 2856 net assigned charge : 1.000008 assigned positive charge : 449.2226 centred at (gu) : 86.33160 88.99352 94.08463 assigned negative charge : -448.2233 centred at (gu) : 86.10386 88.53656 94.14207 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 88660 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23674 grid for indexing accessible points = 1.400000 m= 31425 mr = 64098 m= 4619 mr = 23674 m= 310 mr = 2852 m= 1 mr = 133 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 236 time to turn everything in is 0.5900000 number of dielectric boundary points 34258 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 170 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 22535 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) : 0.6401956 object centre at (A) : 15.73400 -6.9000244E-02 20.61050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.0690671E-03 3.6565051E-03 midg,1,midg; midg,igrid,midg -7.6197139E-03 2.9220903E-02 1,midg,midg; igrid,midg,midg -3.9384250E-02 1.8711004E-02 gauss-seidel spectral radius is 0.9986882 estimated iterations to convergence 219 setup time was (sec) 0.8600000 now iterating at: 14:38:29 rms-change max change #iterations 4.684835 182.9095 at 10iterations 2.237412 65.01456 at 20iterations 1.064443 34.34771 at 30iterations 0.5078306 16.35696 at 40iterations 0.2410725 7.045610 at 50iterations 0.1151178 3.486418 at 60iterations 5.4850474E-02 1.634628 at 70iterations 2.6040705E-02 0.7556601 at 80iterations 1.2425137E-02 0.3362465 at 90iterations 5.9028063E-03 0.1646664 at 100iterations 2.8126433E-03 7.9559326E-02 at 110iterations 1.3423685E-03 3.8043976E-02 at 120iterations finished qdiffx linear iterations at : 14:38:35 total time elapsed so far: 6.930000 # loops : 120 mean,max change (kT/e) : 1.3423685E-03 3.8043976E-02 energy calculations done at 6.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.100000 DelPhi exited at 14:38:36 7.107u 0.213s 0:07.64 95.6% 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 Sat Oct 8 2011 at 14:38:36 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3001 !!! WARNING: NDP 318 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.880880 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): -12.07000 43.53800 ymin,ymax (A): -22.78600 22.64800 zmin,zma (A): -6.399000 47.62000 x,y,z range (A): 55.60800 45.43400 54.01900 scale (grids/A): 2.880880 object centre (A): 15.73400 -6.9000244E-02 20.61050 number of atom coordinates read : 3001 total number of charged atoms : 2856 net assigned charge : 1.000008 assigned positive charge : 449.2226 centred at (gu) : 84.49719 88.49014 96.12685 assigned negative charge : -448.2233 centred at (gu) : 84.15573 87.80474 96.21307 start vw surface at 0.1700000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 205417 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23674 grid for indexing accessible points = 1.400000 m= 103774 mr = 154747 m= 35987 mr = 86557 m= 8270 mr = 29147 m= 1266 mr = 6160 m= 92 mr = 892 m= 0 mr = 53 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 780 time to turn everything in is 1.520000 number of dielectric boundary points 77250 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.660000 number of grid points assigned charge 22847 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) : 1.920587 object centre at (A) : 15.73400 -6.9000244E-02 20.61050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9470987E-02 0.1850722 midg,1,midg; midg,igrid,midg -5.2522026E-02 0.2978196 1,midg,midg; igrid,midg,midg -0.6403250 0.2408718 gauss-seidel spectral radius is 0.9992754 estimated iterations to convergence 293 setup time was (sec) 1.830000 now iterating at: 14:38:38 rms-change max change #iterations 10.82660 386.6139 at 10iterations 6.339401 123.0971 at 20iterations 3.683644 63.67761 at 30iterations 2.140874 41.22880 at 40iterations 1.241050 21.42409 at 50iterations 0.7209674 12.28072 at 60iterations 0.4177295 7.124567 at 70iterations 0.2416161 4.048505 at 80iterations 0.1398733 2.441689 at 90iterations 8.0764711E-02 1.395778 at 100iterations 4.6745360E-02 0.7591133 at 110iterations 2.7053937E-02 0.4719577 at 120iterations 1.5631054E-02 0.2614202 at 130iterations 9.0385405E-03 0.1418333 at 140iterations 5.2252491E-03 8.7554730E-02 at 150iterations 3.0183303E-03 5.5309296E-02 at 160iterations 1.7440842E-03 2.9731750E-02 at 170iterations 1.0109786E-03 1.5603065E-02 at 180iterations finished qdiffx linear iterations at : 14:38:48 total time elapsed so far: 11.59000 # loops : 180 mean,max change (kT/e) : 1.0109786E-03 1.5603065E-02 energy calculations done at 11.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.76000 DelPhi exited at 14:38:48 11.764u 0.212s 0:12.27 97.5% 0+0k 0+0io 0pf+0w