Wed Dec 28 11:03:03 PST 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 Wed Dec 28 2011 at 11:03:04 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 0.6528756 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): -4.459000 34.68100 ymin,ymax (A): -3.417000 47.93200 zmin,zma (A): -23.76800 30.76000 x,y,z range (A): 39.14000 51.34900 54.52800 scale (grids/A): 0.6528756 object centre (A): 15.11100 22.25750 3.496000 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 291.0260 centred at (gu) : 90.27568 92.58253 90.11727 assigned negative charge : -289.0262 centred at (gu) : 90.41063 92.73830 90.04521 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5612 nv = 96 ne = 84 npr = 40890 no. pairs analyzed = 40890 no. exposed pairs = 2481 no. arc points = 17403 no. surface atoms = 832 nbur = 1132 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 335 mr = 3107 m= 3 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 27 time to turn everything in is 0.2800000 number of dielectric boundary points 2798 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1714 ## 155 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 6646 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.9406083E-09 1.3798607E-08 midg,1,midg; midg,igrid,midg 1.3637714E-08 -2.5647097E-08 1,midg,midg; igrid,midg,midg 1.9748521E-08 -1.2596757E-08 gauss-seidel spectral radius is 0.9877849 estimated iterations to convergence 74 setup time was (sec) 0.7500000 now iterating at: 11:03:05 rms-change max change #iterations 0.1378511 24.42670 at 10iterations 1.4333864E-02 2.133572 at 20iterations 1.4614060E-03 0.2151546 at 30iterations 1.4904641E-04 2.8568268E-02 at 40iterations 1.5607769E-05 2.7103424E-03 at 50iterations finished qdiffx linear iterations at : 11:03:12 total time elapsed so far: 8.300000 # loops : 50 mean,max change (kT/e) : 1.5607769E-05 2.7103424E-03 energy calculations done at 8.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.480000 DelPhi exited at 11:03:13 8.489u 0.717s 0:09.59 95.8% 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 Dec 28 2011 at 11:03:13 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 1.958627 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): -4.459000 34.68100 ymin,ymax (A): -3.417000 47.93200 zmin,zma (A): -23.76800 30.76000 x,y,z range (A): 39.14000 51.34900 54.52800 scale (grids/A): 1.958627 object centre (A): 15.11100 22.25750 3.496000 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 291.0260 centred at (gu) : 90.82677 97.74753 90.35194 assigned negative charge : -289.0262 centred at (gu) : 91.23219 98.21502 90.13576 start vw surface at 0.1100000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 60539 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17403 grid for indexing accessible points = 1.400000 m= 21986 mr = 41578 m= 3801 mr = 16606 m= 251 mr = 2541 m= 4 mr = 101 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 975 time to turn everything in is 0.6900000 number of dielectric boundary points 25755 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 116 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 14476 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) : 0.6528756 object centre at (A) : 15.11100 22.25750 3.496000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6788916E-02 1.6683429E-02 midg,1,midg; midg,igrid,midg 4.6708498E-02 -1.2537978E-02 1,midg,midg; igrid,midg,midg 6.5702735E-03 -9.9474546E-03 gauss-seidel spectral radius is 0.9986289 estimated iterations to convergence 214 setup time was (sec) 1.290000 now iterating at: 11:03:15 rms-change max change #iterations 3.839617 157.1967 at 10iterations 1.792087 65.67423 at 20iterations 0.8399470 29.24643 at 30iterations 0.3918310 13.47991 at 40iterations 0.1831508 7.001282 at 50iterations 8.5434794E-02 3.011101 at 60iterations 3.9947446E-02 1.579258 at 70iterations 1.8654654E-02 0.6904602 at 80iterations 8.7407054E-03 0.3067136 at 90iterations 4.0692613E-03 0.1678324 at 100iterations 1.8988447E-03 6.5225601E-02 at 110iterations 8.9049595E-04 3.0998230E-02 at 120iterations finished qdiffx linear iterations at : 11:03:32 total time elapsed so far: 17.98000 # loops : 120 mean,max change (kT/e) : 8.9049595E-04 3.0998230E-02 energy calculations done at 17.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.17000 DelPhi exited at 11:03:33 18.178u 0.800s 0:19.76 96.0% 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 Dec 28 2011 at 11:03:33 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 2.937940 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): -4.459000 34.68100 ymin,ymax (A): -3.417000 47.93200 zmin,zma (A): -23.76800 30.76000 x,y,z range (A): 39.14000 51.34900 54.52800 scale (grids/A): 2.937940 object centre (A): 15.11100 22.25750 3.496000 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 291.0260 centred at (gu) : 91.24031 101.6212 90.52801 assigned negative charge : -289.0262 centred at (gu) : 91.84837 102.3226 90.20358 start vw surface at 0.1200000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 139783 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17403 grid for indexing accessible points = 1.400000 m= 70476 mr = 100524 m= 26470 mr = 58184 m= 7003 mr = 21856 m= 1135 mr = 5546 m= 68 mr = 769 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 3091 time to turn everything in is 1.600000 number of dielectric boundary points 58037 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.840000 number of grid points assigned charge 14656 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) : 1.958627 object centre at (A) : 15.11100 22.25750 3.496000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.097372 3.6474854E-02 midg,1,midg; midg,igrid,midg 0.5034985 -0.1834032 1,midg,midg; igrid,midg,midg 3.1274490E-02 -6.1674837E-02 gauss-seidel spectral radius is 0.9992442 estimated iterations to convergence 287 setup time was (sec) 2.190000 now iterating at: 11:03:36 rms-change max change #iterations 8.855536 409.4377 at 10iterations 5.069925 112.4283 at 20iterations 2.893552 63.38447 at 30iterations 1.651629 32.90295 at 40iterations 0.9428316 18.72093 at 50iterations 0.5362708 10.71756 at 60iterations 0.3057649 7.176914 at 70iterations 0.1742182 3.398880 at 80iterations 9.9337898E-02 2.101738 at 90iterations 5.6517415E-02 1.149628 at 100iterations 3.2200243E-02 0.6778476 at 110iterations 1.8397665E-02 0.3686314 at 120iterations 1.0451383E-02 0.2048326 at 130iterations 5.9566819E-03 0.1176119 at 140iterations 3.3916382E-03 6.1441422E-02 at 150iterations 1.9316354E-03 4.0102959E-02 at 160iterations 1.1033491E-03 2.2696972E-02 at 170iterations 6.2776043E-04 1.1845887E-02 at 180iterations finished qdiffx linear iterations at : 11:04:03 total time elapsed so far: 29.44000 # loops : 180 mean,max change (kT/e) : 6.2776043E-04 1.1845887E-02 energy calculations done at 29.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 29.61000 DelPhi exited at 11:04:04 29.619u 0.868s 0:31.12 97.9% 0+0k 0+0io 0pf+0w