Sun Oct 9 13:09:47 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 Sun Oct 9 2011 at 13:09:47 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2353 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.6797266 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): -6.097000 44.49900 ymin,ymax (A): -14.61000 37.76400 zmin,zma (A): 1.151000 45.90700 x,y,z range (A): 50.59600 52.37400 44.75600 scale (grids/A): 0.6797266 object centre (A): 19.20100 11.57700 23.52900 number of atom coordinates read : 2353 total number of charged atoms : 2212 net assigned charge : 3.500019 assigned positive charge : 360.6111 centred at (gu) : 89.35660 90.91612 90.81294 assigned negative charge : -357.1116 centred at (gu) : 89.35275 91.08702 90.89938 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7578 nv = 96 ne = 84 npr = 45724 no. pairs analyzed = 45724 no. exposed pairs = 2997 no. arc points = 21169 no. surface atoms = 1016 nbur = 1337 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 525 mr = 4214 m= 6 mr = 91 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3804 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2079 ## 190 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8533 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.4947274E-08 -1.2182611E-08 midg,1,midg; midg,igrid,midg 5.4452489E-08 -4.3631559E-08 1,midg,midg; igrid,midg,midg 1.6558058E-08 1.4889173E-08 gauss-seidel spectral radius is 0.9887626 estimated iterations to convergence 77 setup time was (sec) 0.5500000 now iterating at: 13:09:48 rms-change max change #iterations 0.1820708 26.99066 at 10iterations 2.0801783E-02 2.833972 at 20iterations 2.8078216E-03 0.3228912 at 30iterations 5.5432424E-04 7.2921753E-02 at 40iterations 1.5578476E-04 1.9035339E-02 at 50iterations finished qdiffx linear iterations at : 13:09:50 total time elapsed so far: 3.010000 # loops : 50 mean,max change (kT/e) : 1.5578476E-04 1.9035339E-02 energy calculations done at 3.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.190000 DelPhi exited at 13:09:51 3.190u 0.142s 0:03.60 92.5% 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 13:09:51 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2353 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.039180 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): -6.097000 44.49900 ymin,ymax (A): -14.61000 37.76400 zmin,zma (A): 1.151000 45.90700 x,y,z range (A): 50.59600 52.37400 44.75600 scale (grids/A): 2.039180 object centre (A): 19.20100 11.57700 23.52900 number of atom coordinates read : 2353 total number of charged atoms : 2212 net assigned charge : 3.500019 assigned positive charge : 360.6111 centred at (gu) : 88.06947 92.74793 92.43816 assigned negative charge : -357.1116 centred at (gu) : 88.05798 93.26086 92.69803 start vw surface at 0.2100000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 81000 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21169 grid for indexing accessible points = 1.400000 m= 32276 mr = 56201 m= 5779 mr = 24498 m= 487 mr = 3772 m= 11 mr = 208 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 392 time to turn everything in is 0.6300000 number of dielectric boundary points 34874 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 140 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 17515 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) : 0.6797266 object centre at (A) : 19.20100 11.57700 23.52900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6336409E-02 6.9797575E-03 midg,1,midg; midg,igrid,midg 1.6196135E-02 -6.1235245E-02 1,midg,midg; igrid,midg,midg 4.2438567E-02 -1.0850587E-02 gauss-seidel spectral radius is 0.9987862 estimated iterations to convergence 227 setup time was (sec) 0.8900000 now iterating at: 13:09:52 rms-change max change #iterations 4.659245 227.9337 at 10iterations 2.261413 81.75813 at 20iterations 1.108308 36.56614 at 30iterations 0.5405414 16.35422 at 40iterations 0.2645205 7.861214 at 50iterations 0.1295576 4.132206 at 60iterations 6.3529670E-02 2.039513 at 70iterations 3.1265683E-02 0.9665384 at 80iterations 1.5395803E-02 0.4565411 at 90iterations 7.6005552E-03 0.2289085 at 100iterations 3.8173608E-03 0.1146355 at 110iterations 1.9568368E-03 5.7701111E-02 at 120iterations finished qdiffx linear iterations at : 13:09:58 total time elapsed so far: 6.890000 # loops : 120 mean,max change (kT/e) : 1.9568368E-03 5.7701111E-02 energy calculations done at 6.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.070000 DelPhi exited at 13:09:58 7.077u 0.171s 0:07.60 95.2% 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 13:09:58 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2353 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: 3.058770 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): -6.097000 44.49900 ymin,ymax (A): -14.61000 37.76400 zmin,zma (A): 1.151000 45.90700 x,y,z range (A): 50.59600 52.37400 44.75600 scale (grids/A): 3.058770 object centre (A): 19.20100 11.57700 23.52900 number of atom coordinates read : 2353 total number of charged atoms : 2212 net assigned charge : 3.500019 assigned positive charge : 360.6111 centred at (gu) : 87.10408 94.12188 93.65723 assigned negative charge : -357.1116 centred at (gu) : 87.08685 94.89129 94.04699 start vw surface at 0.1900000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 186816 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21169 grid for indexing accessible points = 1.400000 m= 101085 mr = 135929 m= 40350 mr = 83677 m= 10648 mr = 33141 m= 1890 mr = 8147 m= 198 mr = 1312 m= 4 mr = 95 m= 0 mr = 0 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 1545 time to turn everything in is 1.530000 number of dielectric boundary points 78690 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.660000 number of grid points assigned charge 17694 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) : 2.039180 object centre at (A) : 19.20100 11.57700 23.52900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4460696 -3.8826123E-02 midg,1,midg; midg,igrid,midg 0.4316096 -0.7465423 1,midg,midg; igrid,midg,midg 0.4515124 -0.3562998 gauss-seidel spectral radius is 0.9992896 estimated iterations to convergence 296 setup time was (sec) 1.810000 now iterating at: 13:10:00 rms-change max change #iterations 10.67129 433.8245 at 10iterations 6.325773 134.0609 at 20iterations 3.732213 68.31375 at 30iterations 2.203147 39.32789 at 40iterations 1.298011 24.22784 at 50iterations 0.7639124 13.89223 at 60iterations 0.4463217 7.997207 at 70iterations 0.2609664 4.777671 at 80iterations 0.1532060 2.696107 at 90iterations 8.9677922E-02 1.669697 at 100iterations 5.2296661E-02 0.8948958 at 110iterations 3.0662011E-02 0.5309792 at 120iterations 1.8054955E-02 0.3208122 at 130iterations 1.0699566E-02 0.2096100 at 140iterations 6.4308029E-03 0.1142349 at 150iterations 3.9427634E-03 7.7846527E-02 at 160iterations 2.5160767E-03 5.4260254E-02 at 170iterations 1.6821522E-03 3.5705566E-02 at 180iterations finished qdiffx linear iterations at : 13:10:10 total time elapsed so far: 11.33000 # loops : 180 mean,max change (kT/e) : 1.6821522E-03 3.5705566E-02 energy calculations done at 11.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.51000 DelPhi exited at 13:10:10 11.511u 0.170s 0:11.95 97.7% 0+0k 0+0io 0pf+0w