Mon Oct 10 10:23:06 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 10:23:06 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2762 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: 0.5881478 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): -20.15800 40.37100 ymin,ymax (A): -11.29400 43.83200 zmin,zma (A): -1.385000 53.55400 x,y,z range (A): 60.52900 55.12600 54.93900 scale (grids/A): 0.5881478 object centre (A): 10.10650 16.26900 26.08450 number of atom coordinates read : 2762 total number of charged atoms : 2617 net assigned charge : 13.00002 assigned positive charge : 406.4420 centred at (gu) : 91.74899 91.18059 86.27006 assigned negative charge : -393.4425 centred at (gu) : 91.89121 91.23238 86.01975 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6554 nv = 96 ne = 84 npr = 52784 no. pairs analyzed = 52784 no. exposed pairs = 4132 no. arc points = 29752 no. surface atoms = 1367 nbur = 1395 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 324 mr = 2950 m= 2 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3914 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2945 ## 294 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8092 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.2014234E-09 4.3326671E-09 midg,1,midg; midg,igrid,midg 4.0671435E-09 3.5591445E-09 1,midg,midg; igrid,midg,midg 5.0403202E-09 5.6648353E-10 gauss-seidel spectral radius is 0.9850772 estimated iterations to convergence 67 setup time was (sec) 0.3800000 now iterating at: 10:23:06 rms-change max change #iterations 0.1007194 16.05287 at 10iterations 7.9827961E-03 1.364739 at 20iterations 6.6316250E-04 0.1281300 at 30iterations 6.7686902E-05 8.5763931E-03 at 40iterations 1.0879203E-05 1.1061430E-03 at 50iterations finished qdiffx linear iterations at : 10:23:09 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 1.0879203E-05 1.1061430E-03 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 10:23:10 3.401u 0.183s 0:03.88 92.2% 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 10:23:10 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2762 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: 1.764444 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): -20.15800 40.37100 ymin,ymax (A): -11.29400 43.83200 zmin,zma (A): -1.385000 53.55400 x,y,z range (A): 60.52900 55.12600 54.93900 scale (grids/A): 1.764444 object centre (A): 10.10650 16.26900 26.08450 number of atom coordinates read : 2762 total number of charged atoms : 2617 net assigned charge : 13.00002 assigned positive charge : 406.4420 centred at (gu) : 95.24648 93.54147 78.80952 assigned negative charge : -393.4425 centred at (gu) : 95.67348 93.69698 78.05895 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 70109 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29752 grid for indexing accessible points = 1.400000 m= 23004 mr = 43402 m= 3036 mr = 15026 m= 106 mr = 1483 m= 3 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 36332 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 227 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 20346 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) : 0.5881478 object centre at (A) : 10.10650 16.26900 26.08450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9887785E-03 1.9887123E-02 midg,1,midg; midg,igrid,midg 2.2716302E-02 2.9074438E-02 1,midg,midg; igrid,midg,midg 1.5880229E-02 1.8265298E-02 gauss-seidel spectral radius is 0.9984421 estimated iterations to convergence 201 setup time was (sec) 0.5700000 now iterating at: 10:23:11 rms-change max change #iterations 3.697572 149.0157 at 10iterations 1.630457 61.88111 at 20iterations 0.7210171 23.61952 at 30iterations 0.3192396 10.50230 at 40iterations 0.1419293 4.890559 at 50iterations 6.2581696E-02 2.166687 at 60iterations 2.7702212E-02 1.032971 at 70iterations 1.2309191E-02 0.4284096 at 80iterations 5.4499526E-03 0.1804085 at 90iterations 2.4208133E-03 7.8891754E-02 at 100iterations 1.0779992E-03 3.7208557E-02 at 110iterations 4.8026766E-04 1.8363953E-02 at 120iterations finished qdiffx linear iterations at : 10:23:18 total time elapsed so far: 7.690000 # loops : 120 mean,max change (kT/e) : 4.8026766E-04 1.8363953E-02 energy calculations done at 7.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.820000 DelPhi exited at 10:23:18 7.820u 0.207s 0:08.32 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 Mon Oct 10 2011 at 10:23:18 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2762 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: 2.646665 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): -20.15800 40.37100 ymin,ymax (A): -11.29400 43.83200 zmin,zma (A): -1.385000 53.55400 x,y,z range (A): 60.52900 55.12600 54.93900 scale (grids/A): 2.646665 object centre (A): 10.10650 16.26900 26.08450 number of atom coordinates read : 2762 total number of charged atoms : 2617 net assigned charge : 13.00002 assigned positive charge : 406.4420 centred at (gu) : 97.86964 95.31216 73.21420 assigned negative charge : -393.4425 centred at (gu) : 98.51012 95.54550 72.08847 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 162356 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29752 grid for indexing accessible points = 1.400000 m= 74771 mr = 107312 m= 25040 mr = 56583 m= 4875 mr = 18216 m= 475 mr = 3129 m= 14 mr = 219 m= 0 mr = 2 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9000000 number of dielectric boundary points 82070 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 20932 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) : 1.764444 object centre at (A) : 10.10650 16.26900 26.08450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.6179355E-02 0.2116618 midg,1,midg; midg,igrid,midg 0.3633069 0.3221233 1,midg,midg; igrid,midg,midg 0.2698577 0.2923669 gauss-seidel spectral radius is 0.9992241 estimated iterations to convergence 283 setup time was (sec) 1.140000 now iterating at: 10:23:20 rms-change max change #iterations 9.480726 279.3816 at 10iterations 5.627344 191.6177 at 20iterations 3.289972 81.34100 at 30iterations 1.904469 49.85163 at 40iterations 1.100114 29.34419 at 50iterations 0.6325991 16.21674 at 60iterations 0.3620170 8.443299 at 70iterations 0.2072590 4.471840 at 80iterations 0.1180293 2.855998 at 90iterations 6.7361675E-02 1.388071 at 100iterations 3.8349714E-02 0.8294106 at 110iterations 2.1761144E-02 0.4744072 at 120iterations 1.2389120E-02 0.2545977 at 130iterations 7.0294570E-03 0.1446743 at 140iterations 3.9884802E-03 8.1627816E-02 at 150iterations 2.2638664E-03 5.0670147E-02 at 160iterations 1.2841031E-03 2.5975704E-02 at 170iterations 7.3056103E-04 1.4644623E-02 at 180iterations finished qdiffx linear iterations at : 10:23:31 total time elapsed so far: 12.57000 # loops : 180 mean,max change (kT/e) : 7.3056103E-04 1.4644623E-02 energy calculations done at 12.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.70000 DelPhi exited at 10:23:31 12.706u 0.197s 0:13.17 97.8% 0+0k 0+0io 0pf+0w