Mon Oct 10 13:58:14 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 13:58:14 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: 242 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2777 !!! WARNING: PRO 436 has a net charge of 0.5000 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: 0.6177553 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): -13.61100 44.01700 ymin,ymax (A): -28.60600 22.38000 zmin,zma (A): 21.26200 68.38500 x,y,z range (A): 57.62800 50.98600 47.12300 scale (grids/A): 0.6177553 object centre (A): 15.20300 -3.113000 44.82350 number of atom coordinates read : 2777 total number of charged atoms : 2631 net assigned charge : 3.500010 assigned positive charge : 422.1672 centred at (gu) : 89.42077 89.49926 90.12343 assigned negative charge : -418.6683 centred at (gu) : 89.41264 89.59834 89.95109 start vw surface at 0.1800000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7045 nv = 96 ne = 84 npr = 55349 no. pairs analyzed = 55349 no. exposed pairs = 3563 no. arc points = 25176 no. surface atoms = 1194 nbur = 1583 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 356 mr = 3661 m= 4 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 77 time to turn everything in is 0.3300000 number of dielectric boundary points 3707 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2615 ## 274 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8688 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.9554257E-09 1.4339916E-08 midg,1,midg; midg,igrid,midg 1.0258240E-08 -3.6823438E-09 1,midg,midg; igrid,midg,midg 2.3136795E-09 2.7723512E-09 gauss-seidel spectral radius is 0.9864496 estimated iterations to convergence 70 setup time was (sec) 0.5500000 now iterating at: 13:58:15 rms-change max change #iterations 0.1283824 21.95796 at 10iterations 1.1483710E-02 1.577522 at 20iterations 1.0646760E-03 0.1734762 at 30iterations 1.0385965E-04 1.6895294E-02 at 40iterations 1.4821268E-05 2.8710365E-03 at 50iterations finished qdiffx linear iterations at : 13:58:18 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 1.4821268E-05 2.8710365E-03 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 13:58:18 3.345u 0.146s 0:04.01 86.7% 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 Mon Oct 10 2011 at 13:58:18 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: 242 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2777 !!! WARNING: PRO 436 has a net charge of 0.5000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.853266 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): -13.61100 44.01700 ymin,ymax (A): -28.60600 22.38000 zmin,zma (A): 21.26200 68.38500 x,y,z range (A): 57.62800 50.98600 47.12300 scale (grids/A): 1.853266 object centre (A): 15.20300 -3.113000 44.82350 number of atom coordinates read : 2777 total number of charged atoms : 2631 net assigned charge : 3.500010 assigned positive charge : 422.1672 centred at (gu) : 88.26144 88.49695 90.36935 assigned negative charge : -418.6683 centred at (gu) : 88.23733 88.79474 89.85306 start vw surface at 0.2500000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 76230 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25176 grid for indexing accessible points = 1.400000 m= 26497 mr = 51651 m= 3778 mr = 18726 m= 204 mr = 2139 m= 3 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 815 time to turn everything in is 0.6600000 number of dielectric boundary points 34145 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 204 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 20583 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) : 0.6177553 object centre at (A) : 15.20300 -3.113000 44.82350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5296432E-03 1.6728260E-02 midg,1,midg; midg,igrid,midg 3.0959861E-02 1.3382732E-02 1,midg,midg; igrid,midg,midg -4.1049186E-02 -9.0344073E-03 gauss-seidel spectral radius is 0.9985885 estimated iterations to convergence 211 setup time was (sec) 0.9500000 now iterating at: 13:58:19 rms-change max change #iterations 4.187510 165.3170 at 10iterations 1.927952 66.36252 at 20iterations 0.8863912 30.24244 at 30iterations 0.4101250 12.56968 at 40iterations 0.1890483 5.921989 at 50iterations 8.7574519E-02 2.741082 at 60iterations 4.0336184E-02 1.234882 at 70iterations 1.8645523E-02 0.5891914 at 80iterations 8.6070923E-03 0.2854509 at 90iterations 3.9845523E-03 0.1278162 at 100iterations 1.8401988E-03 5.8882713E-02 at 110iterations 8.5378240E-04 2.8823853E-02 at 120iterations finished qdiffx linear iterations at : 13:58:26 total time elapsed so far: 7.330000 # loops : 120 mean,max change (kT/e) : 8.5378240E-04 2.8823853E-02 energy calculations done at 7.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.520000 DelPhi exited at 13:58:26 7.523u 0.220s 0:08.14 95.0% 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 13:58:27 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: 242 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2777 !!! WARNING: PRO 436 has a net charge of 0.5000 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: 2.779899 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): -13.61100 44.01700 ymin,ymax (A): -28.60600 22.38000 zmin,zma (A): 21.26200 68.38500 x,y,z range (A): 57.62800 50.98600 47.12300 scale (grids/A): 2.779899 object centre (A): 15.20300 -3.113000 44.82350 number of atom coordinates read : 2777 total number of charged atoms : 2631 net assigned charge : 3.500010 assigned positive charge : 422.1672 centred at (gu) : 87.39186 87.74516 90.55402 assigned negative charge : -418.6683 centred at (gu) : 87.35601 88.19219 89.77945 start vw surface at 0.1500000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 176375 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25176 grid for indexing accessible points = 1.400000 m= 87406 mr = 125652 m= 29569 mr = 70233 m= 6547 mr = 22928 m= 846 mr = 4567 m= 38 mr = 514 m= 0 mr = 5 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 2699 time to turn everything in is 1.450000 number of dielectric boundary points 76882 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 21037 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) : 1.853266 object centre at (A) : 15.20300 -3.113000 44.82350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9788401E-02 0.1019911 midg,1,midg; midg,igrid,midg 0.3585944 0.1584196 1,midg,midg; igrid,midg,midg -0.6176941 3.0757533E-02 gauss-seidel spectral radius is 0.9992531 estimated iterations to convergence 289 setup time was (sec) 1.780000 now iterating at: 13:58:28 rms-change max change #iterations 10.10354 285.3639 at 10iterations 5.965841 125.4235 at 20iterations 3.499255 96.35684 at 30iterations 2.033873 46.30084 at 40iterations 1.181720 23.45646 at 50iterations 0.6840445 12.62705 at 60iterations 0.3953479 8.563129 at 70iterations 0.2283131 4.158220 at 80iterations 0.1314929 2.419281 at 90iterations 7.5825714E-02 1.615349 at 100iterations 4.3495364E-02 0.7887459 at 110iterations 2.5014408E-02 0.4742742 at 120iterations 1.4410391E-02 0.3078156 at 130iterations 8.2802083E-03 0.1504974 at 140iterations 4.7612339E-03 8.1477642E-02 at 150iterations 2.7469196E-03 5.1399231E-02 at 160iterations 1.5844068E-03 3.0587196E-02 at 170iterations 9.2284492E-04 1.7830372E-02 at 180iterations finished qdiffx linear iterations at : 13:58:40 total time elapsed so far: 12.87000 # loops : 180 mean,max change (kT/e) : 9.2284492E-04 1.7830372E-02 energy calculations done at 12.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.05000 DelPhi exited at 13:58:40 13.056u 0.251s 0:13.76 96.6% 0+0k 0+0io 0pf+0w