Mon Oct 10 00:03:02 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 Mon Oct 10 2011 at 00:03:02 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2570 !!! WARNING: SEP 674 has a net charge of -0.4750 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: 0.6211506 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): -7.854000 49.45900 ymin,ymax (A): -27.35200 22.85700 zmin,zma (A): -7.570000 40.40900 x,y,z range (A): 57.31300 50.20900 47.97900 scale (grids/A): 0.6211506 object centre (A): 20.80250 -2.247499 16.41950 number of atom coordinates read : 2570 total number of charged atoms : 2429 net assigned charge : 2.525008 assigned positive charge : 390.8739 centred at (gu) : 89.71922 90.82858 87.92678 assigned negative charge : -388.3497 centred at (gu) : 89.61121 90.89331 87.91047 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6442 nv = 96 ne = 84 npr = 52640 no. pairs analyzed = 52640 no. exposed pairs = 3172 no. arc points = 22205 no. surface atoms = 1070 nbur = 1500 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 268 mr = 3450 m= 2 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 24 time to turn everything in is 0.2100000 number of dielectric boundary points 3244 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2270 ## 233 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7993 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6347557E-09 2.1195485E-09 midg,1,midg; midg,igrid,midg 5.4900426E-09 -2.7590088E-09 1,midg,midg; igrid,midg,midg -5.6367688E-09 8.9151211E-09 gauss-seidel spectral radius is 0.9865727 estimated iterations to convergence 71 setup time was (sec) 0.4000000 now iterating at: 00:03:02 rms-change max change #iterations 0.1269665 18.28674 at 10iterations 1.1561384E-02 1.760830 at 20iterations 1.0678509E-03 0.1504259 at 30iterations 9.9636236E-05 1.3671875E-02 at 40iterations 9.0922640E-06 1.3847351E-03 at 50iterations finished qdiffx linear iterations at : 00:03:05 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 9.0922640E-06 1.3847351E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 00:03:06 3.415u 0.157s 0:03.85 92.4% 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 00:03:06 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2570 !!! WARNING: SEP 674 has a net charge of -0.4750 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: 1.863452 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): -7.854000 49.45900 ymin,ymax (A): -27.35200 22.85700 zmin,zma (A): -7.570000 40.40900 x,y,z range (A): 57.31300 50.20900 47.97900 scale (grids/A): 1.863452 object centre (A): 20.80250 -2.247499 16.41950 number of atom coordinates read : 2570 total number of charged atoms : 2429 net assigned charge : 2.525008 assigned positive charge : 390.8739 centred at (gu) : 89.15702 92.48552 83.77984 assigned negative charge : -388.3497 centred at (gu) : 88.83338 92.67975 83.73129 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 70232 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22205 grid for indexing accessible points = 1.400000 m= 22805 mr = 47826 m= 2787 mr = 16413 m= 111 mr = 1618 m= 0 mr = 37 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 489 time to turn everything in is 0.3600000 number of dielectric boundary points 30041 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 207 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 19032 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) : 0.6211506 object centre at (A) : 20.80250 -2.247499 16.41950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1728070E-02 1.6479280E-03 midg,1,midg; midg,igrid,midg 8.4274765E-03 3.0436928E-03 1,midg,midg; igrid,midg,midg -2.5933361E-02 3.6047250E-02 gauss-seidel spectral radius is 0.9985645 estimated iterations to convergence 209 setup time was (sec) 0.5700000 now iterating at: 00:03:06 rms-change max change #iterations 4.054152 174.5227 at 10iterations 1.852974 67.73431 at 20iterations 0.8501970 27.99533 at 30iterations 0.3889795 14.66538 at 40iterations 0.1792809 5.675145 at 50iterations 8.2181670E-02 2.697052 at 60iterations 3.7649725E-02 1.251122 at 70iterations 1.7299147E-02 0.5761948 at 80iterations 7.9293409E-03 0.2556648 at 90iterations 3.6499295E-03 0.1147966 at 100iterations 1.6770527E-03 5.6227684E-02 at 110iterations 7.6647848E-04 2.9434487E-02 at 120iterations finished qdiffx linear iterations at : 00:03:13 total time elapsed so far: 7.640000 # loops : 120 mean,max change (kT/e) : 7.6647848E-04 2.9434487E-02 energy calculations done at 7.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 00:03:14 7.775u 0.185s 0:08.28 96.0% 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 00:03:14 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2570 !!! WARNING: SEP 674 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.795177 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): -7.854000 49.45900 ymin,ymax (A): -27.35200 22.85700 zmin,zma (A): -7.570000 40.40900 x,y,z range (A): 57.31300 50.20900 47.97900 scale (grids/A): 2.795177 object centre (A): 20.80250 -2.247499 16.41950 number of atom coordinates read : 2570 total number of charged atoms : 2429 net assigned charge : 2.525008 assigned positive charge : 390.8739 centred at (gu) : 88.73539 93.72808 80.66973 assigned negative charge : -388.3497 centred at (gu) : 88.24996 94.01973 80.59681 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 162749 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22205 grid for indexing accessible points = 1.400000 m= 76729 mr = 116460 m= 24589 mr = 61973 m= 4698 mr = 19444 m= 491 mr = 3411 m= 23 mr = 297 m= 0 mr = 12 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 1609 time to turn everything in is 0.8600000 number of dielectric boundary points 67682 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 19431 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) : 1.863452 object centre at (A) : 20.80250 -2.247499 16.41950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1180315 1.8775996E-02 midg,1,midg; midg,igrid,midg 8.4574200E-02 0.1208218 1,midg,midg; igrid,midg,midg -0.3220015 0.4536768 gauss-seidel spectral radius is 0.9992426 estimated iterations to convergence 287 setup time was (sec) 1.080000 now iterating at: 00:03:15 rms-change max change #iterations 9.539449 350.4729 at 10iterations 5.485462 120.0290 at 20iterations 3.129291 62.92920 at 30iterations 1.784675 35.00438 at 40iterations 1.018412 21.24701 at 50iterations 0.5797909 10.94080 at 60iterations 0.3295698 6.320529 at 70iterations 0.1875001 3.796610 at 80iterations 0.1069191 2.138100 at 90iterations 6.0706381E-02 1.153333 at 100iterations 3.4650330E-02 0.6818943 at 110iterations 1.9707959E-02 0.3643638 at 120iterations 1.1235784E-02 0.2110577 at 130iterations 6.3928762E-03 0.1232529 at 140iterations 3.6372812E-03 6.7645073E-02 at 150iterations 2.0721282E-03 3.8584948E-02 at 160iterations 1.1808473E-03 2.3429394E-02 at 170iterations 6.7096268E-04 1.1503458E-02 at 180iterations finished qdiffx linear iterations at : 00:03:27 total time elapsed so far: 12.35000 # loops : 180 mean,max change (kT/e) : 6.7096268E-04 1.1503458E-02 energy calculations done at 12.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.48000 DelPhi exited at 00:03:27 12.486u 0.227s 0:12.98 97.8% 0+0k 0+0io 0pf+0w