Tue Oct 11 08:21:27 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 08:21:27 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: 227 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1176 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7430909 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): -6.937000 31.09100 ymin,ymax (A): 1.195000 39.63400 zmin,zma (A): -1.868000 46.04000 x,y,z range (A): 38.02800 38.43900 47.90800 scale (grids/A): 0.7430909 object centre (A): 12.07700 20.41450 22.08600 number of atom coordinates read : 1176 total number of charged atoms : 1061 net assigned charge : 5.500003 assigned positive charge : 175.3231 centred at (gu) : 89.06009 89.23977 88.52676 assigned negative charge : -169.8232 centred at (gu) : 88.74401 89.20935 88.55122 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 4411 nv = 96 ne = 84 npr = 23175 no. pairs analyzed = 23175 no. exposed pairs = 1491 no. arc points = 10836 no. surface atoms = 504 nbur = 672 mkacc time = 5.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 273 mr = 2310 m= 0 mr = 52 time to grow re-entrant surface = 6.0000010E-02 no. cavity mid-points inaccessible to solvent = 36 time to turn everything in is 0.1800000 number of dielectric boundary points 2322 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 816 ## 61 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 4442 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5624852E-07 7.0512314E-08 midg,1,midg; midg,igrid,midg 1.0076070E-07 1.0704323E-07 1,midg,midg; igrid,midg,midg -9.8331007E-08 2.3583728E-07 gauss-seidel spectral radius is 0.9904657 estimated iterations to convergence 83 setup time was (sec) 0.3900000 now iterating at: 08:21:28 rms-change max change #iterations 0.1797440 34.04884 at 10iterations 2.4464468E-02 4.155602 at 20iterations 3.2643145E-03 0.6669164 at 30iterations 4.4669461E-04 8.6479187E-02 at 40iterations 5.8781992E-05 8.9912415E-03 at 50iterations finished qdiffx linear iterations at : 08:21:31 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 5.8781992E-05 8.9912415E-03 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.130000 DelPhi exited at 08:21:31 3.136u 0.168s 0:03.73 88.2% 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 Tue Oct 11 2011 at 08:21:31 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: 227 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1176 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: 2.229273 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): -6.937000 31.09100 ymin,ymax (A): 1.195000 39.63400 zmin,zma (A): -1.868000 46.04000 x,y,z range (A): 38.02800 38.43900 47.90800 scale (grids/A): 2.229273 object centre (A): 12.07700 20.41450 22.08600 number of atom coordinates read : 1176 total number of charged atoms : 1061 net assigned charge : 5.500003 assigned positive charge : 175.3231 centred at (gu) : 87.18044 87.71947 85.58051 assigned negative charge : -169.8232 centred at (gu) : 86.23228 87.62814 85.65385 start vw surface at 0.1200000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 45893 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10836 grid for indexing accessible points = 1.400000 m= 17117 mr = 30177 m= 3330 mr = 12794 m= 359 mr = 2290 m= 21 mr = 205 m= 0 mr = 13 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 1058 time to turn everything in is 0.3600000 number of dielectric boundary points 21241 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 32 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8457 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) : 0.7430909 object centre at (A) : 12.07700 20.41450 22.08600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9322552E-02 1.2040474E-02 midg,1,midg; midg,igrid,midg 3.7574198E-02 3.4103997E-02 1,midg,midg; igrid,midg,midg -3.0617896E-02 3.9826535E-02 gauss-seidel spectral radius is 0.9988409 estimated iterations to convergence 232 setup time was (sec) 0.6300000 now iterating at: 08:21:32 rms-change max change #iterations 3.618188 214.7652 at 10iterations 1.798927 76.78745 at 20iterations 0.8908819 35.89248 at 30iterations 0.4429895 16.17256 at 40iterations 0.2194461 9.301041 at 50iterations 0.1089928 4.031761 at 60iterations 5.3966384E-02 2.014748 at 70iterations 2.6708459E-02 1.027290 at 80iterations 1.3316033E-02 0.4655433 at 90iterations 6.5876474E-03 0.2529287 at 100iterations 3.2729278E-03 0.1277761 at 110iterations 1.6162058E-03 5.8137894E-02 at 120iterations finished qdiffx linear iterations at : 08:21:38 total time elapsed so far: 6.450000 # loops : 120 mean,max change (kT/e) : 1.6162058E-03 5.8137894E-02 energy calculations done at 6.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.620000 DelPhi exited at 08:21:38 6.626u 0.156s 0:07.16 94.5% 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 08:21:38 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: 227 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1176 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.343909 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): -6.937000 31.09100 ymin,ymax (A): 1.195000 39.63400 zmin,zma (A): -1.868000 46.04000 x,y,z range (A): 38.02800 38.43900 47.90800 scale (grids/A): 3.343909 object centre (A): 12.07700 20.41450 22.08600 number of atom coordinates read : 1176 total number of charged atoms : 1061 net assigned charge : 5.500003 assigned positive charge : 175.3231 centred at (gu) : 85.77065 86.57926 83.37074 assigned negative charge : -169.8232 centred at (gu) : 84.34848 86.44221 83.48079 start vw surface at 0.1400000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 105607 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10836 grid for indexing accessible points = 1.400000 m= 53106 mr = 72810 m= 21688 mr = 43547 m= 6405 mr = 17914 m= 1332 mr = 5040 m= 200 mr = 1015 m= 29 mr = 148 m= 0 mr = 26 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 3344 time to turn everything in is 1.080000 number of dielectric boundary points 47867 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 8488 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) : 2.229273 object centre at (A) : 12.07700 20.41450 22.08600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2186291 0.1279454 midg,1,midg; midg,igrid,midg 0.3334014 0.2843605 1,midg,midg; igrid,midg,midg -0.2533950 0.2700251 gauss-seidel spectral radius is 0.9992912 estimated iterations to convergence 296 setup time was (sec) 1.340000 now iterating at: 08:21:40 rms-change max change #iterations 7.863388 287.6089 at 10iterations 4.589162 151.5310 at 20iterations 2.656356 60.96288 at 30iterations 1.532708 31.29362 at 40iterations 0.8888186 19.34266 at 50iterations 0.5149384 11.19776 at 60iterations 0.2983513 6.302532 at 70iterations 0.1726445 3.810752 at 80iterations 0.1000058 2.213516 at 90iterations 5.7968479E-02 1.284248 at 100iterations 3.3631276E-02 0.7627888 at 110iterations 1.9450832E-02 0.3923187 at 120iterations 1.1278396E-02 0.2502804 at 130iterations 6.5430333E-03 0.1472912 at 140iterations 3.7894247E-03 8.4845312E-02 at 150iterations 2.1955636E-03 4.7520638E-02 at 160iterations 1.2714943E-03 3.0338287E-02 at 170iterations 7.3864445E-04 1.6361237E-02 at 180iterations finished qdiffx linear iterations at : 08:21:49 total time elapsed so far: 10.36000 # loops : 180 mean,max change (kT/e) : 7.3864445E-04 1.6361237E-02 energy calculations done at 10.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.53000 DelPhi exited at 08:21:50 10.537u 0.190s 0:11.34 94.5% 0+0k 0+0io 0pf+0w