Tue Oct 11 05:18:19 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 Tue Oct 11 2011 at 05:18:19 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2306 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: MG5 577 has a net charge of 1.4000 !!! WARNING: ZN5 578 has a net charge of 1.4000 !!! WARNING: ZN5 579 has a net charge of 1.4000 !!! WARNING: ZN5 580 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6895349 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): 15.65800 62.97800 ymin,ymax (A): -3.554000 33.68100 zmin,zma (A): 20.16900 71.79800 x,y,z range (A): 47.32000 37.23500 51.62901 scale (grids/A): 0.6895349 object centre (A): 39.31800 15.06350 45.98350 number of atom coordinates read : 2306 total number of charged atoms : 1982 net assigned charge : 11.32501 assigned positive charge : 326.7039 centred at (gu) : 91.47519 89.76957 89.21408 assigned negative charge : -315.3791 centred at (gu) : 91.55881 89.71108 89.10258 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6774 nv = 96 ne = 84 npr = 42618 no. pairs analyzed = 42618 no. exposed pairs = 2514 no. arc points = 17392 no. surface atoms = 860 nbur = 1446 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 430 mr = 3922 m= 1 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3202 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1707 ## 185 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7705 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9070398E-08 8.4942570E-08 midg,1,midg; midg,igrid,midg 4.5069189E-08 7.8252661E-08 1,midg,midg; igrid,midg,midg 6.7592971E-08 4.5594881E-08 gauss-seidel spectral radius is 0.9890431 estimated iterations to convergence 78 setup time was (sec) 0.4900000 now iterating at: 05:18:19 rms-change max change #iterations 0.1906331 26.58419 at 10iterations 2.2216156E-02 2.955833 at 20iterations 2.5696601E-03 0.3353043 at 30iterations 3.1360277E-04 5.2901268E-02 at 40iterations 4.0888383E-05 5.7573318E-03 at 50iterations finished qdiffx linear iterations at : 05:18:22 total time elapsed so far: 2.870000 # loops : 50 mean,max change (kT/e) : 4.0888383E-05 5.7573318E-03 energy calculations done at 2.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.050000 DelPhi exited at 05:18:22 3.052u 0.130s 0:03.50 90.8% 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 Tue Oct 11 2011 at 05:18:22 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2306 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: MG5 577 has a net charge of 1.4000 !!! WARNING: ZN5 578 has a net charge of 1.4000 !!! WARNING: ZN5 579 has a net charge of 1.4000 !!! WARNING: ZN5 580 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.068605 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): 15.65800 62.97800 ymin,ymax (A): -3.554000 33.68100 zmin,zma (A): 20.16900 71.79800 x,y,z range (A): 47.32000 37.23500 51.62901 scale (grids/A): 2.068605 object centre (A): 39.31800 15.06350 45.98350 number of atom coordinates read : 2306 total number of charged atoms : 1982 net assigned charge : 11.32501 assigned positive charge : 326.7039 centred at (gu) : 94.42549 89.30853 87.64204 assigned negative charge : -315.3791 centred at (gu) : 94.67654 89.13340 87.30771 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 72302 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17392 grid for indexing accessible points = 1.400000 m= 28745 mr = 51642 m= 5364 mr = 22026 m= 435 mr = 3602 m= 5 mr = 218 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 29363 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 90 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 15732 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) : 0.6895349 object centre at (A) : 39.31800 15.06350 45.98350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.8809592E-02 5.8902957E-02 midg,1,midg; midg,igrid,midg 3.0908950E-02 4.6772499E-02 1,midg,midg; igrid,midg,midg 2.6676722E-02 3.5660487E-02 gauss-seidel spectral radius is 0.9987768 estimated iterations to convergence 226 setup time was (sec) 0.7900000 now iterating at: 05:18:23 rms-change max change #iterations 4.470624 223.3245 at 10iterations 2.192183 78.03188 at 20iterations 1.063496 31.65459 at 30iterations 0.5200404 16.94267 at 40iterations 0.2530887 8.311163 at 50iterations 0.1240688 3.923351 at 60iterations 6.0519658E-02 1.878761 at 70iterations 2.9614229E-02 1.098091 at 80iterations 1.4461956E-02 0.5117168 at 90iterations 7.0605157E-03 0.2028255 at 100iterations 3.4500954E-03 0.1086161 at 110iterations 1.6880311E-03 4.9102783E-02 at 120iterations finished qdiffx linear iterations at : 05:18:29 total time elapsed so far: 6.640000 # loops : 120 mean,max change (kT/e) : 1.6880311E-03 4.9102783E-02 energy calculations done at 6.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.810000 DelPhi exited at 05:18:29 6.809u 0.174s 0:07.28 95.7% 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 05:18:30 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2306 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: MG5 577 has a net charge of 1.4000 !!! WARNING: ZN5 578 has a net charge of 1.4000 !!! WARNING: ZN5 579 has a net charge of 1.4000 !!! WARNING: ZN5 580 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.102907 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): 15.65800 62.97800 ymin,ymax (A): -3.554000 33.68100 zmin,zma (A): 20.16900 71.79800 x,y,z range (A): 47.32000 37.23500 51.62901 scale (grids/A): 3.102907 object centre (A): 39.31800 15.06350 45.98350 number of atom coordinates read : 2306 total number of charged atoms : 1982 net assigned charge : 11.32501 assigned positive charge : 326.7039 centred at (gu) : 96.63826 88.96280 86.46302 assigned negative charge : -315.3791 centred at (gu) : 97.01482 88.70014 85.96156 start vw surface at 0.1700000 fill in re-entrant regions at 0.7500000 boundary points on vw surface= 166840 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17392 grid for indexing accessible points = 1.400000 m= 90622 mr = 124648 m= 35517 mr = 75616 m= 10068 mr = 29274 m= 1918 mr = 7891 m= 181 mr = 1428 m= 4 mr = 116 m= 0 mr = 0 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.630000 number of dielectric boundary points 66177 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.750000 number of grid points assigned charge 15856 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) : 2.068605 object centre at (A) : 39.31800 15.06350 45.98350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5008883 0.4678127 midg,1,midg; midg,igrid,midg 0.2865716 0.4137762 1,midg,midg; igrid,midg,midg 0.2225002 0.5898960 gauss-seidel spectral radius is 0.9992821 estimated iterations to convergence 295 setup time was (sec) 1.900000 now iterating at: 05:18:32 rms-change max change #iterations 10.09022 393.2297 at 10iterations 5.938551 141.2052 at 20iterations 3.494550 68.82440 at 30iterations 2.044667 42.05025 at 40iterations 1.196912 27.55728 at 50iterations 0.7019429 12.67453 at 60iterations 0.4087035 8.319758 at 70iterations 0.2381415 4.362305 at 80iterations 0.1393522 2.645470 at 90iterations 8.0853030E-02 1.575470 at 100iterations 4.7059041E-02 0.9368153 at 110iterations 2.7376497E-02 0.4742908 at 120iterations 1.5960075E-02 0.2896042 at 130iterations 9.2952661E-03 0.1747932 at 140iterations 5.4207011E-03 9.4791412E-02 at 150iterations 3.1730866E-03 5.6236267E-02 at 160iterations 1.8623210E-03 3.4442902E-02 at 170iterations 1.1055255E-03 2.0814896E-02 at 180iterations finished qdiffx linear iterations at : 05:18:41 total time elapsed so far: 11.10000 # loops : 180 mean,max change (kT/e) : 1.1055255E-03 2.0814896E-02 energy calculations done at 11.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.27000 DelPhi exited at 05:18:42 11.272u 0.165s 0:12.01 95.1% 0+0k 0+0io 0pf+0w