Tue Oct 11 08:37:09 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 Tue Oct 11 2011 at 08:37:09 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3002 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.6489009 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): -11.03600 37.32300 ymin,ymax (A): -25.87800 22.28700 zmin,zma (A): -8.748000 46.11400 x,y,z range (A): 48.35900 48.16500 54.86200 scale (grids/A): 0.6489009 object centre (A): 13.14350 -1.795501 18.68300 number of atom coordinates read : 3002 total number of charged atoms : 2611 net assigned charge : 3.500026 assigned positive charge : 415.4985 centred at (gu) : 89.97639 90.41625 91.19771 assigned negative charge : -411.9993 centred at (gu) : 89.73881 90.27065 91.24897 start vw surface at 0.1800000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7761 nv = 96 ne = 84 npr = 56670 no. pairs analyzed = 56670 no. exposed pairs = 3388 no. arc points = 23606 no. surface atoms = 1140 nbur = 1862 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 411 mr = 4333 m= 2 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3789 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2375 ## 225 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9293 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1398503E-08 -2.0269237E-09 midg,1,midg; midg,igrid,midg -1.5152740E-08 3.1853055E-08 1,midg,midg; igrid,midg,midg -3.1828506E-08 4.2793904E-08 gauss-seidel spectral radius is 0.9877056 estimated iterations to convergence 74 setup time was (sec) 0.5700000 now iterating at: 08:37:09 rms-change max change #iterations 0.1569135 24.57071 at 10iterations 1.6628835E-02 2.845678 at 20iterations 1.8034778E-03 0.2491646 at 30iterations 2.3336499E-04 3.8108826E-02 at 40iterations 4.6440131E-05 7.6503754E-03 at 50iterations finished qdiffx linear iterations at : 08:37:12 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 4.6440131E-05 7.6503754E-03 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 08:37:13 3.361u 0.166s 0:04.02 87.5% 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 Tue Oct 11 2011 at 08:37:13 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3002 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: 1.946703 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): -11.03600 37.32300 ymin,ymax (A): -25.87800 22.28700 zmin,zma (A): -8.748000 46.11400 x,y,z range (A): 48.35900 48.16500 54.86200 scale (grids/A): 1.946703 object centre (A): 13.14350 -1.795501 18.68300 number of atom coordinates read : 3002 total number of charged atoms : 2611 net assigned charge : 3.500026 assigned positive charge : 415.4985 centred at (gu) : 89.92844 91.24800 93.59252 assigned negative charge : -411.9993 centred at (gu) : 89.21601 90.81189 93.74670 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 83877 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23606 grid for indexing accessible points = 1.400000 m= 30464 mr = 58999 m= 4660 mr = 22589 m= 299 mr = 2942 m= 1 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 293 time to turn everything in is 0.6200000 number of dielectric boundary points 34665 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 132 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 20443 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) : 0.6489009 object centre at (A) : 13.14350 -1.795501 18.68300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.2229382E-03 -1.5236487E-02 midg,1,midg; midg,igrid,midg -9.8947044E-03 2.6283124E-02 1,midg,midg; igrid,midg,midg -1.2857410E-02 5.8040045E-02 gauss-seidel spectral radius is 0.9987095 estimated iterations to convergence 221 setup time was (sec) 0.9000000 now iterating at: 08:37:14 rms-change max change #iterations 4.581122 195.0315 at 10iterations 2.200884 68.29133 at 20iterations 1.052719 31.87625 at 30iterations 0.5042313 14.95822 at 40iterations 0.2418887 7.815240 at 50iterations 0.1159970 3.339320 at 60iterations 5.5714209E-02 1.586214 at 70iterations 2.6641363E-02 0.8173194 at 80iterations 1.2746770E-02 0.3816795 at 90iterations 6.1427490E-03 0.1861095 at 100iterations 2.9548844E-03 9.4905853E-02 at 110iterations 1.4359580E-03 4.4668198E-02 at 120iterations finished qdiffx linear iterations at : 08:37:20 total time elapsed so far: 7.310000 # loops : 120 mean,max change (kT/e) : 1.4359580E-03 4.4668198E-02 energy calculations done at 7.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.500000 DelPhi exited at 08:37:21 7.503u 0.170s 0:07.96 96.3% 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 Tue Oct 11 2011 at 08:37:21 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3002 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: 2.920054 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): -11.03600 37.32300 ymin,ymax (A): -25.87800 22.28700 zmin,zma (A): -8.748000 46.11400 x,y,z range (A): 48.35900 48.16500 54.86200 scale (grids/A): 2.920054 object centre (A): 13.14350 -1.795501 18.68300 number of atom coordinates read : 3002 total number of charged atoms : 2611 net assigned charge : 3.500026 assigned positive charge : 415.4985 centred at (gu) : 89.89250 91.87175 95.38866 assigned negative charge : -411.9993 centred at (gu) : 88.82397 91.21770 95.61987 start vw surface at 0.1700000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 193933 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23606 grid for indexing accessible points = 1.400000 m= 99450 mr = 142709 m= 35621 mr = 81807 m= 8532 mr = 28765 m= 1248 mr = 6374 m= 87 mr = 844 m= 0 mr = 39 time to grow re-entrant surface = 0.9299999 no. cavity mid-points inaccessible to solvent = 1071 time to turn everything in is 1.580000 number of dielectric boundary points 78333 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.710000 number of grid points assigned charge 20880 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) : 1.946703 object centre at (A) : 13.14350 -1.795501 18.68300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1748198 2.6900817E-02 midg,1,midg; midg,igrid,midg -0.1348220 0.3232239 1,midg,midg; igrid,midg,midg -8.6133845E-02 0.5185459 gauss-seidel spectral radius is 0.9992764 estimated iterations to convergence 293 setup time was (sec) 1.880000 now iterating at: 08:37:23 rms-change max change #iterations 10.48074 373.8745 at 10iterations 6.151540 134.1305 at 20iterations 3.591995 79.39832 at 30iterations 2.095142 44.50412 at 40iterations 1.220237 23.63358 at 50iterations 0.7108903 12.59939 at 60iterations 0.4127058 7.312764 at 70iterations 0.2396134 4.417072 at 80iterations 0.1393773 2.380040 at 90iterations 8.0670357E-02 1.406477 at 100iterations 4.6846751E-02 0.8281288 at 110iterations 2.7178746E-02 0.4732981 at 120iterations 1.5820928E-02 0.2969284 at 130iterations 9.1781355E-03 0.1500549 at 140iterations 5.3698770E-03 9.2395782E-02 at 150iterations 3.1525709E-03 5.4635048E-02 at 160iterations 1.8770550E-03 3.3969879E-02 at 170iterations 1.1325956E-03 2.0509362E-02 at 180iterations finished qdiffx linear iterations at : 08:37:33 total time elapsed so far: 12.03000 # loops : 180 mean,max change (kT/e) : 1.1325956E-03 2.0509362E-02 energy calculations done at 12.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.23000 DelPhi exited at 08:37:34 12.230u 0.190s 0:12.92 96.1% 0+0k 0+0io 0pf+0w