Wed Feb 15 08:54:37 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:54:37 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2731 !!! WARNING: ADP 662 has a net charge of -2.0000 !!! WARNING: MG6 664 has a net charge of 1.4000 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: 0.5918832 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): -7.958000 52.18900 ymin,ymax (A): -16.17900 34.45800 zmin,zma (A): 77.42900 129.9400 x,y,z range (A): 60.14700 50.63700 52.51100 scale (grids/A): 0.5918832 object centre (A): 22.11550 9.139500 103.6845 number of atom coordinates read : 2731 total number of charged atoms : 2589 net assigned charge : -3.599991 assigned positive charge : 423.3494 centred at (gu) : 91.98691 89.62823 89.41725 assigned negative charge : -426.9503 centred at (gu) : 91.92326 89.71574 89.49067 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6321 nv = 96 ne = 84 npr = 54962 no. pairs analyzed = 54962 no. exposed pairs = 3761 no. arc points = 25964 no. surface atoms = 1263 nbur = 1468 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 333 mr = 3179 m= 1 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3442 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2625 ## 284 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 7949 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1706522E-09 -3.0927956E-09 midg,1,midg; midg,igrid,midg 1.5782879E-09 -3.6538519E-09 1,midg,midg; igrid,midg,midg -2.0553477E-09 1.1891479E-09 gauss-seidel spectral radius is 0.9852445 estimated iterations to convergence 68 setup time was (sec) 0.4500000 now iterating at: 08:54:38 rms-change max change #iterations 0.1062683 19.44731 at 10iterations 8.7284725E-03 1.386487 at 20iterations 7.2525395E-04 0.1195183 at 30iterations 7.6862561E-05 1.3244629E-02 at 40iterations 1.3592658E-05 2.1162033E-03 at 50iterations finished qdiffx linear iterations at : 08:54:42 total time elapsed so far: 4.570000 # loops : 50 mean,max change (kT/e) : 1.3592658E-05 2.1162033E-03 energy calculations done at 4.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.700000 DelPhi exited at 08:54:42 4.708u 0.271s 0:05.31 93.5% 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 Wed Feb 15 2012 at 08:54:42 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2731 !!! WARNING: ADP 662 has a net charge of -2.0000 !!! WARNING: MG6 664 has a net charge of 1.4000 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: 1.775650 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): -7.958000 52.18900 ymin,ymax (A): -16.17900 34.45800 zmin,zma (A): 77.42900 129.9400 x,y,z range (A): 60.14700 50.63700 52.51100 scale (grids/A): 1.775650 object centre (A): 22.11550 9.139500 103.6845 number of atom coordinates read : 2731 total number of charged atoms : 2589 net assigned charge : -3.599991 assigned positive charge : 423.3494 centred at (gu) : 95.96011 88.88414 88.25081 assigned negative charge : -426.9503 centred at (gu) : 95.76930 89.14703 88.47173 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 68432 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25964 grid for indexing accessible points = 1.400000 m= 23131 mr = 45314 m= 3233 mr = 15894 m= 161 mr = 1728 m= 1 mr = 29 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 0.3900000 number of dielectric boundary points 31993 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 223 iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 20183 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) : 0.5918832 object centre at (A) : 22.11550 9.139500 103.6845 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.2005711E-03 -2.9731704E-02 midg,1,midg; midg,igrid,midg -6.8146749E-03 -1.7513791E-02 1,midg,midg; igrid,midg,midg 1.8417859E-02 3.2137953E-02 gauss-seidel spectral radius is 0.9984566 estimated iterations to convergence 202 setup time was (sec) 0.8100000 now iterating at: 08:54:44 rms-change max change #iterations 3.942451 192.1109 at 10iterations 1.757710 62.74557 at 20iterations 0.7812732 28.16870 at 30iterations 0.3490953 13.45600 at 40iterations 0.1556983 5.993605 at 50iterations 6.9823503E-02 2.388920 at 60iterations 3.0977763E-02 1.072619 at 70iterations 1.3870974E-02 0.4561844 at 80iterations 6.1884704E-03 0.1950207 at 90iterations 2.7799162E-03 9.0112686E-02 at 100iterations 1.2393151E-03 4.7697425E-02 at 110iterations 5.5994536E-04 1.9699097E-02 at 120iterations finished qdiffx linear iterations at : 08:54:53 total time elapsed so far: 9.860000 # loops : 120 mean,max change (kT/e) : 5.5994536E-04 1.9699097E-02 energy calculations done at 9.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.00000 DelPhi exited at 08:54:56 10.000u 0.497s 0:14.05 74.6% 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 Wed Feb 15 2012 at 08:54:57 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2731 !!! WARNING: ADP 662 has a net charge of -2.0000 !!! WARNING: MG6 664 has a net charge of 1.4000 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: 2.663474 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): -7.958000 52.18900 ymin,ymax (A): -16.17900 34.45800 zmin,zma (A): 77.42900 129.9400 x,y,z range (A): 60.14700 50.63700 52.51100 scale (grids/A): 2.663474 object centre (A): 22.11550 9.139500 103.6845 number of atom coordinates read : 2731 total number of charged atoms : 2589 net assigned charge : -3.599991 assigned positive charge : 423.3494 centred at (gu) : 98.94003 88.32603 87.37611 assigned negative charge : -426.9503 centred at (gu) : 98.65377 88.72051 87.70747 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 158411 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25964 grid for indexing accessible points = 1.400000 m= 76137 mr = 111057 m= 25468 mr = 59315 m= 5466 mr = 19373 m= 618 mr = 3760 m= 16 mr = 346 m= 0 mr = 0 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9600000 number of dielectric boundary points 72265 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.130000 number of grid points assigned charge 20706 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) : 1.775650 object centre at (A) : 22.11550 9.139500 103.6845 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.9006891E-02 -0.3818204 midg,1,midg; midg,igrid,midg -0.1081486 -0.1793036 1,midg,midg; igrid,midg,midg 0.3701025 0.3135787 gauss-seidel spectral radius is 0.9992208 estimated iterations to convergence 283 setup time was (sec) 1.380000 now iterating at: 08:54:58 rms-change max change #iterations 9.771221 325.0654 at 10iterations 5.685485 148.2007 at 20iterations 3.279663 74.72794 at 30iterations 1.882555 42.12555 at 40iterations 1.074811 22.25155 at 50iterations 0.6139728 12.40991 at 60iterations 0.3495476 7.518524 at 70iterations 0.1990494 4.023483 at 80iterations 0.1130997 2.570560 at 90iterations 6.4025380E-02 1.346809 at 100iterations 3.6438569E-02 0.6710777 at 110iterations 2.0644950E-02 0.4035426 at 120iterations 1.1666190E-02 0.2432480 at 130iterations 6.6263932E-03 0.1398404 at 140iterations 3.7532919E-03 6.9042206E-02 at 150iterations 2.1267673E-03 3.9840698E-02 at 160iterations 1.2101649E-03 2.5966644E-02 at 170iterations 6.8729883E-04 1.4986038E-02 at 180iterations finished qdiffx linear iterations at : 08:55:13 total time elapsed so far: 16.39000 # loops : 180 mean,max change (kT/e) : 6.8729883E-04 1.4986038E-02 energy calculations done at 16.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.53000 DelPhi exited at 08:55:14 16.532u 0.351s 0:17.81 94.7% 0+0k 0+0io 0pf+0w