Tue Oct 11 06:27:36 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 06:27:36 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 = 1334 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.8054116 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): -14.80500 25.59100 ymin,ymax (A): 42.08600 76.46600 zmin,zma (A): -4.739000 39.46200 x,y,z range (A): 40.39600 34.38000 44.20100 scale (grids/A): 0.8054116 object centre (A): 5.393000 59.27600 17.36150 number of atom coordinates read : 1334 total number of charged atoms : 1268 net assigned charge : 2.500002 assigned positive charge : 201.4374 centred at (gu) : 89.98721 90.19032 89.75974 assigned negative charge : -198.9373 centred at (gu) : 90.13032 90.24774 89.47505 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6453 nv = 96 ne = 84 npr = 25147 no. pairs analyzed = 25147 no. exposed pairs = 1693 no. arc points = 12129 no. surface atoms = 589 nbur = 745 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 540 mr = 3700 m= 6 mr = 143 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3156 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 879 ## 64 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 6086 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.8374699E-07 7.3181553E-07 midg,1,midg; midg,igrid,midg 2.7948224E-07 4.2557364E-08 1,midg,midg; igrid,midg,midg 4.7096313E-07 -1.4589918E-07 gauss-seidel spectral radius is 0.9918812 estimated iterations to convergence 90 setup time was (sec) 0.5100000 now iterating at: 06:27:37 rms-change max change #iterations 0.2666317 37.29942 at 10iterations 4.1564971E-02 6.431046 at 20iterations 6.6382685E-03 0.9057875 at 30iterations 1.1085031E-03 0.1516266 at 40iterations 2.2099282E-04 3.6861420E-02 at 50iterations finished qdiffx linear iterations at : 06:27:40 total time elapsed so far: 3.820000 # loops : 50 mean,max change (kT/e) : 2.2099282E-04 3.6861420E-02 energy calculations done at 3.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.000000 DelPhi exited at 06:27:40 4.008u 0.246s 0:04.66 90.9% 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 06:27:41 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 = 1334 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.416235 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): -14.80500 25.59100 ymin,ymax (A): 42.08600 76.46600 zmin,zma (A): -4.739000 39.46200 x,y,z range (A): 40.39600 34.38000 44.20100 scale (grids/A): 2.416235 object centre (A): 5.393000 59.27600 17.36150 number of atom coordinates read : 1334 total number of charged atoms : 1268 net assigned charge : 2.500002 assigned positive charge : 201.4374 centred at (gu) : 89.96208 90.57133 89.27963 assigned negative charge : -198.9373 centred at (gu) : 90.39114 90.74366 88.42559 start vw surface at 0.1100000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 67022 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12129 grid for indexing accessible points = 1.400000 m= 29586 mr = 47187 m= 7512 mr = 23072 m= 1015 mr = 5523 m= 74 mr = 641 m= 2 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 28749 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 24 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 10127 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) : 0.8054116 object centre at (A) : 5.393000 59.27600 17.36150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.8968565E-02 7.5068377E-02 midg,1,midg; midg,igrid,midg 3.0214500E-02 4.2815125E-03 1,midg,midg; igrid,midg,midg 8.1220731E-02 1.1658587E-02 gauss-seidel spectral radius is 0.9989983 estimated iterations to convergence 250 setup time was (sec) 0.9100000 now iterating at: 06:27:42 rms-change max change #iterations 4.516087 235.1499 at 10iterations 2.372172 76.45283 at 20iterations 1.240110 41.01902 at 30iterations 0.6457736 20.08706 at 40iterations 0.3384390 10.26074 at 50iterations 0.1773834 5.438405 at 60iterations 9.2435762E-02 3.081888 at 70iterations 4.8382547E-02 1.419338 at 80iterations 2.5416337E-02 0.8211004 at 90iterations 1.3352765E-02 0.3980293 at 100iterations 7.0319385E-03 0.2154808 at 110iterations 3.7313607E-03 0.1190958 at 120iterations finished qdiffx linear iterations at : 06:27:50 total time elapsed so far: 9.270000 # loops : 120 mean,max change (kT/e) : 3.7313607E-03 0.1190958 energy calculations done at 9.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.450000 DelPhi exited at 06:27:51 9.454u 0.339s 0:10.28 95.1% 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 06:27:51 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 = 1334 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.624352 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): -14.80500 25.59100 ymin,ymax (A): 42.08600 76.46600 zmin,zma (A): -4.739000 39.46200 x,y,z range (A): 40.39600 34.38000 44.20100 scale (grids/A): 3.624352 object centre (A): 5.393000 59.27600 17.36150 number of atom coordinates read : 1334 total number of charged atoms : 1268 net assigned charge : 2.500002 assigned positive charge : 201.4374 centred at (gu) : 89.94322 90.85710 88.91948 assigned negative charge : -198.9373 centred at (gu) : 90.58669 91.11545 87.63844 start vw surface at 0.1300000 fill in re-entrant regions at 0.8800000 boundary points on vw surface= 153849 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12129 grid for indexing accessible points = 1.400000 m= 87324 mr = 112866 m= 41499 mr = 73678 m= 15088 mr = 35207 m= 3957 mr = 12287 m= 735 mr = 3115 m= 106 mr = 543 m= 4 mr = 83 m= 0 mr = 2 time to grow re-entrant surface = 1.080000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.070000 number of dielectric boundary points 64781 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.220000 number of grid points assigned charge 10144 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) : 2.416235 object centre at (A) : 5.393000 59.27600 17.36150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7850387 0.5022762 midg,1,midg; midg,igrid,midg 0.1891782 4.0027637E-02 1,midg,midg; igrid,midg,midg 0.6426901 1.3162553E-02 gauss-seidel spectral radius is 0.9993278 estimated iterations to convergence 304 setup time was (sec) 2.400000 now iterating at: 06:27:53 rms-change max change #iterations 9.575177 317.9312 at 10iterations 5.780234 140.2412 at 20iterations 3.460623 75.19232 at 30iterations 2.072078 43.26074 at 40iterations 1.231943 25.61713 at 50iterations 0.7330711 13.90552 at 60iterations 0.4355980 7.784256 at 70iterations 0.2584714 5.160856 at 80iterations 0.1537742 2.816109 at 90iterations 9.0922885E-02 1.657875 at 100iterations 5.3859282E-02 0.9995947 at 110iterations 3.1879533E-02 0.5428405 at 120iterations 1.8946406E-02 0.3302650 at 130iterations 1.1210660E-02 0.1897388 at 140iterations 6.6306326E-03 0.1127472 at 150iterations 3.9296104E-03 8.3724976E-02 at 160iterations 2.3407785E-03 4.1149139E-02 at 170iterations 1.3987689E-03 3.0196190E-02 at 180iterations finished qdiffx linear iterations at : 06:28:07 total time elapsed so far: 16.05000 # loops : 180 mean,max change (kT/e) : 1.3987689E-03 3.0196190E-02 energy calculations done at 16.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.23000 DelPhi exited at 06:28:08 16.236u 0.303s 0:16.84 98.1% 0+0k 0+0io 0pf+0w