Sun Oct 9 22:10:49 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 Sun Oct 9 2011 at 22:10:49 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3103 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5850068 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): -24.28000 36.57400 ymin,ymax (A): -38.57700 19.10900 zmin,zma (A): -1.331000 51.14400 x,y,z range (A): 60.85400 57.68600 52.47500 scale (grids/A): 0.5850068 object centre (A): 6.146998 -9.734000 24.90650 number of atom coordinates read : 3103 total number of charged atoms : 3032 net assigned charge : 5.500016 assigned positive charge : 483.4167 centred at (gu) : 91.91699 90.94830 89.60928 assigned negative charge : -477.9181 centred at (gu) : 91.96514 90.99778 89.62303 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7040 nv = 96 ne = 84 npr = 58991 no. pairs analyzed = 58991 no. exposed pairs = 4297 no. arc points = 30754 no. surface atoms = 1426 nbur = 1677 mkacc time = 0.1200000 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= 323 mr = 3472 m= 3 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.3300000 number of dielectric boundary points 3873 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3152 ## 411 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 9153 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0159248E-09 9.9159114E-10 midg,1,midg; midg,igrid,midg 2.2752473E-09 8.3022582E-11 1,midg,midg; igrid,midg,midg 1.8034321E-09 1.3754764E-10 gauss-seidel spectral radius is 0.9849352 estimated iterations to convergence 67 setup time was (sec) 0.5500000 now iterating at: 22:10:50 rms-change max change #iterations 0.1028258 16.43239 at 10iterations 8.0601722E-03 1.531521 at 20iterations 6.4907334E-04 0.1106415 at 30iterations 5.2236253E-05 8.1729889E-03 at 40iterations 4.2492193E-06 6.1416626E-04 at 50iterations finished qdiffx linear iterations at : 22:10:53 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 4.2492193E-06 6.1416626E-04 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 22:10:53 3.314u 0.226s 0:03.90 90.5% 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 Sun Oct 9 2011 at 22:10:53 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3103 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.755020 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): -24.28000 36.57400 ymin,ymax (A): -38.57700 19.10900 zmin,zma (A): -1.331000 51.14400 x,y,z range (A): 60.85400 57.68600 52.47500 scale (grids/A): 1.755020 object centre (A): 6.146998 -9.734000 24.90650 number of atom coordinates read : 3103 total number of charged atoms : 3032 net assigned charge : 5.500016 assigned positive charge : 483.4167 centred at (gu) : 95.75016 92.84441 88.82698 assigned negative charge : -477.9181 centred at (gu) : 95.89529 92.99306 88.86839 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 76939 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30754 grid for indexing accessible points = 1.400000 m= 24387 mr = 50264 m= 3046 mr = 16503 m= 121 mr = 1594 m= 0 mr = 16 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 36116 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 332 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 23582 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) : 0.5850068 object centre at (A) : 6.146998 -9.734000 24.90650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3377526E-03 -8.3361159E-04 midg,1,midg; midg,igrid,midg -1.4721539E-03 3.0227988E-03 1,midg,midg; igrid,midg,midg -1.4276913E-02 6.1351866E-03 gauss-seidel spectral radius is 0.9984638 estimated iterations to convergence 202 setup time was (sec) 0.8100000 now iterating at: 22:10:54 rms-change max change #iterations 3.999623 164.7592 at 10iterations 1.769258 65.14391 at 20iterations 0.7873294 30.93348 at 30iterations 0.3514888 10.81898 at 40iterations 0.1565481 4.969982 at 50iterations 6.9963641E-02 2.440025 at 60iterations 3.1183135E-02 1.124931 at 70iterations 1.3861531E-02 0.4306889 at 80iterations 6.2243170E-03 0.2051659 at 90iterations 2.7664921E-03 0.1006165 at 100iterations 1.2369485E-03 4.3386459E-02 at 110iterations 5.5329804E-04 1.9668579E-02 at 120iterations finished qdiffx linear iterations at : 22:11:01 total time elapsed so far: 7.310000 # loops : 120 mean,max change (kT/e) : 5.5329804E-04 1.9668579E-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) 7.480000 DelPhi exited at 22:11:01 7.482u 0.265s 0:08.04 96.2% 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 Sun Oct 9 2011 at 22:11:01 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3103 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: 2.632530 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): -24.28000 36.57400 ymin,ymax (A): -38.57700 19.10900 zmin,zma (A): -1.331000 51.14400 x,y,z range (A): 60.85400 57.68600 52.47500 scale (grids/A): 2.632530 object centre (A): 6.146998 -9.734000 24.90650 number of atom coordinates read : 3103 total number of charged atoms : 3032 net assigned charge : 5.500016 assigned positive charge : 483.4167 centred at (gu) : 98.62505 94.26646 88.24021 assigned negative charge : -477.9181 centred at (gu) : 98.84286 94.48962 88.30248 start vw surface at 0.1300000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 178514 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30754 grid for indexing accessible points = 1.400000 m= 82077 mr = 123270 m= 25457 mr = 64073 m= 5025 mr = 18967 m= 466 mr = 3393 m= 11 mr = 256 m= 0 mr = 0 time to grow re-entrant surface = 0.7500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.270000 number of dielectric boundary points 81591 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.420000 number of grid points assigned charge 24245 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) : 1.755020 object centre at (A) : 6.146998 -9.734000 24.90650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1247820 3.0248845E-02 midg,1,midg; midg,igrid,midg 4.6990567E-04 -0.1163544 1,midg,midg; igrid,midg,midg -0.3196331 4.3761913E-02 gauss-seidel spectral radius is 0.9992363 estimated iterations to convergence 286 setup time was (sec) 1.590000 now iterating at: 22:11:03 rms-change max change #iterations 10.04775 302.1274 at 10iterations 5.909059 138.0491 at 20iterations 3.443923 84.12380 at 30iterations 2.002046 45.36365 at 40iterations 1.154402 25.59464 at 50iterations 0.6665791 13.45481 at 60iterations 0.3829899 8.625389 at 70iterations 0.2196689 4.957226 at 80iterations 0.1259930 2.389282 at 90iterations 7.2058424E-02 1.400692 at 100iterations 4.1190930E-02 0.8220119 at 110iterations 2.3539113E-02 0.4366031 at 120iterations 1.3438191E-02 0.2720642 at 130iterations 7.6720943E-03 0.1622620 at 140iterations 4.3784594E-03 0.1021543 at 150iterations 2.4945943E-03 4.7860563E-02 at 160iterations 1.4214318E-03 2.5441527E-02 at 170iterations 8.1177586E-04 1.5172243E-02 at 180iterations finished qdiffx linear iterations at : 22:11:15 total time elapsed so far: 13.17000 # loops : 180 mean,max change (kT/e) : 8.1177586E-04 1.5172243E-02 energy calculations done at 13.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.33000 DelPhi exited at 22:11:15 13.335u 0.268s 0:13.91 97.6% 0+0k 0+0io 0pf+0w