Tue Oct 11 05:59:51 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 05:59:51 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 = 2020 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: 0.7062511 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): -19.89600 27.38900 ymin,ymax (A): -9.967999 28.51400 zmin,zma (A): -3.192000 47.21500 x,y,z range (A): 47.28500 38.48200 50.40700 scale (grids/A): 0.7062511 object centre (A): 3.746500 9.273001 22.01150 number of atom coordinates read : 2020 total number of charged atoms : 1925 net assigned charge : 6.500009 assigned positive charge : 311.5790 centred at (gu) : 89.04673 89.14246 90.48151 assigned negative charge : -305.0792 centred at (gu) : 88.92900 89.15374 90.55923 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6878 nv = 96 ne = 84 npr = 39729 no. pairs analyzed = 39729 no. exposed pairs = 2498 no. arc points = 17169 no. surface atoms = 850 nbur = 1170 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 455 mr = 3896 m= 4 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3362 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1622 ## 154 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 7681 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.2277957E-08 1.8618968E-08 midg,1,midg; midg,igrid,midg 6.9839430E-08 4.1527478E-08 1,midg,midg; igrid,midg,midg -3.1220104E-09 9.0435421E-08 gauss-seidel spectral radius is 0.9895443 estimated iterations to convergence 80 setup time was (sec) 0.3500000 now iterating at: 05:59:51 rms-change max change #iterations 0.1938353 26.68068 at 10iterations 2.3986371E-02 3.510727 at 20iterations 3.0594158E-03 0.4710007 at 30iterations 4.2688305E-04 6.2887192E-02 at 40iterations 8.2565522E-05 1.2771606E-02 at 50iterations finished qdiffx linear iterations at : 05:59:54 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 8.2565522E-05 1.2771606E-02 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 05:59:55 3.305u 0.175s 0:04.16 83.4% 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 Tue Oct 11 2011 at 05:59:55 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 = 2020 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: 2.118753 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): -19.89600 27.38900 ymin,ymax (A): -9.967999 28.51400 zmin,zma (A): -3.192000 47.21500 x,y,z range (A): 47.28500 38.48200 50.40700 scale (grids/A): 2.118753 object centre (A): 3.746500 9.273001 22.01150 number of atom coordinates read : 2020 total number of charged atoms : 1925 net assigned charge : 6.500009 assigned positive charge : 311.5790 centred at (gu) : 87.14014 87.42723 91.44447 assigned negative charge : -305.0792 centred at (gu) : 86.78718 87.46112 91.67780 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 72959 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17169 grid for indexing accessible points = 1.400000 m= 29290 mr = 51546 m= 5720 mr = 22256 m= 495 mr = 3714 m= 8 mr = 225 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 30731 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 86 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 15274 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) : 0.7062511 object centre at (A) : 3.746500 9.273001 22.01150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1602526E-02 6.1351959E-02 midg,1,midg; midg,igrid,midg 3.1057255E-02 7.4165389E-03 1,midg,midg; igrid,midg,midg 2.6566084E-02 3.0934047E-02 gauss-seidel spectral radius is 0.9988227 estimated iterations to convergence 231 setup time was (sec) 0.5700000 now iterating at: 05:59:56 rms-change max change #iterations 4.510386 184.0735 at 10iterations 2.234990 70.78322 at 20iterations 1.102353 34.50544 at 30iterations 0.5466802 18.04534 at 40iterations 0.2716896 8.492420 at 50iterations 0.1341375 4.233276 at 60iterations 6.6495821E-02 1.965642 at 70iterations 3.2949608E-02 1.046467 at 80iterations 1.6356878E-02 0.4890187 at 90iterations 8.1279846E-03 0.2726374 at 100iterations 4.0405137E-03 0.1328306 at 110iterations 2.0432000E-03 6.5301895E-02 at 120iterations finished qdiffx linear iterations at : 06:00:03 total time elapsed so far: 7.540000 # loops : 120 mean,max change (kT/e) : 2.0432000E-03 6.5301895E-02 energy calculations done at 7.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.670000 DelPhi exited at 06:00:03 7.671u 0.207s 0:08.20 95.9% 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 06:00:03 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 = 2020 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: 3.178130 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): -19.89600 27.38900 ymin,ymax (A): -9.967999 28.51400 zmin,zma (A): -3.192000 47.21500 x,y,z range (A): 47.28500 38.48200 50.40700 scale (grids/A): 3.178130 object centre (A): 3.746500 9.273001 22.01150 number of atom coordinates read : 2020 total number of charged atoms : 1925 net assigned charge : 6.500009 assigned positive charge : 311.5790 centred at (gu) : 85.71029 86.14081 92.16665 assigned negative charge : -305.0792 centred at (gu) : 85.18069 86.19177 92.51678 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 168054 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17169 grid for indexing accessible points = 1.400000 m= 91391 mr = 123963 m= 37415 mr = 76166 m= 10689 mr = 30539 m= 2098 mr = 8191 m= 244 mr = 1544 m= 3 mr = 145 m= 0 mr = 2 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.110000 number of dielectric boundary points 69344 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.200000 number of grid points assigned charge 15400 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) : 2.118753 object centre at (A) : 3.746500 9.273001 22.01150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3287704 0.9187738 midg,1,midg; midg,igrid,midg 0.2512591 4.3934170E-02 1,midg,midg; igrid,midg,midg 0.4255705 0.2660953 gauss-seidel spectral radius is 0.9992943 estimated iterations to convergence 297 setup time was (sec) 1.340000 now iterating at: 06:00:05 rms-change max change #iterations 10.12532 354.9523 at 10iterations 5.985606 122.1013 at 20iterations 3.520096 67.40555 at 30iterations 2.074753 38.01037 at 40iterations 1.219092 25.06577 at 50iterations 0.7148162 12.66196 at 60iterations 0.4191230 8.136057 at 70iterations 0.2455675 4.433121 at 80iterations 0.1436295 2.598431 at 90iterations 8.3952144E-02 1.490504 at 100iterations 4.9183074E-02 0.8486872 at 110iterations 2.8807389E-02 0.5736313 at 120iterations 1.6968168E-02 0.2911034 at 130iterations 1.0066031E-02 0.1947784 at 140iterations 6.0444814E-03 0.1231985 at 150iterations 3.6882907E-03 7.1472168E-02 at 160iterations 2.3488661E-03 4.1145325E-02 at 170iterations 1.5698575E-03 3.0258179E-02 at 180iterations finished qdiffx linear iterations at : 06:00:16 total time elapsed so far: 12.40000 # loops : 180 mean,max change (kT/e) : 1.5698575E-03 3.0258179E-02 energy calculations done at 12.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.53000 DelPhi exited at 06:00:17 12.530u 0.209s 0:13.23 96.2% 0+0k 0+0io 0pf+0w