Tue Oct 11 06:28:08 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 Tue Oct 11 2011 at 06:28:08 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 = 1334 !!! WARNING: SEP 98 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= 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 : 1266 net assigned charge : 2.025002 assigned positive charge : 202.1574 centred at (gu) : 89.96561 90.16682 89.74999 assigned negative charge : -200.1323 centred at (gu) : 90.10437 90.19908 89.45985 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 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 = 7.0000000E-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= 878 ## 64 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 6077 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.3388021E-07 7.1501438E-07 midg,1,midg; midg,igrid,midg 1.9869678E-07 6.6402990E-08 1,midg,midg; igrid,midg,midg 4.3419240E-07 -1.6838986E-07 gauss-seidel spectral radius is 0.9918812 estimated iterations to convergence 90 setup time was (sec) 0.4800000 now iterating at: 06:28:09 rms-change max change #iterations 0.2717345 37.29942 at 10iterations 4.2232193E-02 6.949711 at 20iterations 6.8269488E-03 0.8779421 at 30iterations 1.1998867E-03 0.1698933 at 40iterations 2.7609256E-04 4.6447754E-02 at 50iterations finished qdiffx linear iterations at : 06:28:12 total time elapsed so far: 3.790000 # loops : 50 mean,max change (kT/e) : 2.7609256E-04 4.6447754E-02 energy calculations done at 3.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.980000 DelPhi exited at 06:28:13 3.979u 0.274s 0:04.68 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 Tue Oct 11 2011 at 06:28:13 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1334 !!! WARNING: SEP 98 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= 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 : 1266 net assigned charge : 2.025002 assigned positive charge : 202.1574 centred at (gu) : 89.89724 90.50088 89.25041 assigned negative charge : -200.1323 centred at (gu) : 90.31330 90.59762 88.37998 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 0.7600000 number of grid points assigned charge 10111 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 -0.1012190 7.4278720E-02 midg,1,midg; midg,igrid,midg 1.7463049E-02 3.9095622E-03 1,midg,midg; igrid,midg,midg 8.0976747E-02 1.0475348E-02 gauss-seidel spectral radius is 0.9989983 estimated iterations to convergence 250 setup time was (sec) 0.9300000 now iterating at: 06:28:14 rms-change max change #iterations 4.553992 235.1499 at 10iterations 2.391967 76.45285 at 20iterations 1.249650 41.07770 at 30iterations 0.6509753 20.11558 at 40iterations 0.3413154 10.14827 at 50iterations 0.1789470 5.490577 at 60iterations 9.3253553E-02 3.135475 at 70iterations 4.8859525E-02 1.434564 at 80iterations 2.5717951E-02 0.8303599 at 90iterations 1.3560446E-02 0.3974733 at 100iterations 7.2066234E-03 0.2228985 at 110iterations 3.8834240E-03 0.1184635 at 120iterations finished qdiffx linear iterations at : 06:28:22 total time elapsed so far: 9.260000 # loops : 120 mean,max change (kT/e) : 3.8834240E-03 0.1184635 energy calculations done at 9.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.440000 DelPhi exited at 06:28:23 9.444u 0.305s 0:10.39 93.7% 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 06:28:23 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 = 1334 !!! WARNING: SEP 98 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= 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 : 1266 net assigned charge : 2.025002 assigned positive charge : 202.1574 centred at (gu) : 89.84595 90.75142 88.87563 assigned negative charge : -200.1323 centred at (gu) : 90.46999 90.89640 87.57001 start vw surface at 0.1300000 fill in re-entrant regions at 0.8900000 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 = 1.070000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.060000 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 2.210000 number of grid points assigned charge 10128 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 -0.7988575 0.4979692 midg,1,midg; midg,igrid,midg 9.6866280E-02 3.7780702E-02 1,midg,midg; igrid,midg,midg 0.6447530 7.0332722E-03 gauss-seidel spectral radius is 0.9993278 estimated iterations to convergence 304 setup time was (sec) 2.380000 now iterating at: 06:28:26 rms-change max change #iterations 9.646758 321.5278 at 10iterations 5.821848 143.3577 at 20iterations 3.485916 75.19550 at 30iterations 2.086643 43.63342 at 40iterations 1.240717 26.05623 at 50iterations 0.7382715 13.94064 at 60iterations 0.4387660 7.809258 at 70iterations 0.2602998 5.304690 at 80iterations 0.1548827 2.860826 at 90iterations 9.1574341E-02 1.649910 at 100iterations 5.4259151E-02 1.038995 at 110iterations 3.2129452E-02 0.5503364 at 120iterations 1.9112492E-02 0.3235130 at 130iterations 1.1326656E-02 0.1900387 at 140iterations 6.7255404E-03 0.1143717 at 150iterations 4.0190495E-03 8.2695007E-02 at 160iterations 2.4341065E-03 4.2026520E-02 at 170iterations 1.5054792E-03 3.0988693E-02 at 180iterations finished qdiffx linear iterations at : 06:28:40 total time elapsed so far: 16.08000 # loops : 180 mean,max change (kT/e) : 1.5054792E-03 3.0988693E-02 energy calculations done at 16.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.25000 DelPhi exited at 06:28:40 16.255u 0.327s 0:17.03 97.2% 0+0k 0+0io 0pf+0w