Sat Oct 8 16:23:55 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 Sat Oct 8 2011 at 16:23:55 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2395 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 has a net charge of -0.0940 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: 0.5842387 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): -2.480000 46.55700 ymin,ymax (A): -15.54100 29.74100 zmin,zma (A): -18.98200 41.95200 x,y,z range (A): 49.03700 45.28200 60.93400 scale (grids/A): 0.5842387 object centre (A): 22.03850 7.100000 11.48500 number of atom coordinates read : 2395 total number of charged atoms : 2284 net assigned charge : 3.806002 assigned positive charge : 354.4140 centred at (gu) : 90.22618 88.71571 88.88589 assigned negative charge : -350.6088 centred at (gu) : 90.25381 88.85183 88.91072 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5190 nv = 96 ne = 84 npr = 49647 no. pairs analyzed = 49647 no. exposed pairs = 2887 no. arc points = 19822 no. surface atoms = 986 nbur = 1409 mkacc time = 0.1400000 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 = 1.456000 m= 213 mr = 2788 m= 0 mr = 19 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 19 time to turn everything in is 0.3100000 number of dielectric boundary points 2596 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2053 ## 217 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 6797 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8240010E-09 3.3452244E-10 midg,1,midg; midg,igrid,midg 4.8517026E-09 -1.3470477E-09 1,midg,midg; igrid,midg,midg 1.3924756E-09 3.8356979E-10 gauss-seidel spectral radius is 0.9848236 estimated iterations to convergence 67 setup time was (sec) 0.6000000 now iterating at: 16:23:56 rms-change max change #iterations 9.1198429E-02 18.78179 at 10iterations 7.3420368E-03 1.261431 at 20iterations 6.2336883E-04 0.1208706 at 30iterations 7.9618410E-05 1.7740726E-02 at 40iterations 1.6751395E-05 4.1103363E-03 at 50iterations finished qdiffx linear iterations at : 16:23:59 total time elapsed so far: 3.940000 # loops : 50 mean,max change (kT/e) : 1.6751395E-05 4.1103363E-03 energy calculations done at 3.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.110000 DelPhi exited at 16:24:00 4.113u 0.290s 0:04.71 93.4% 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 Sat Oct 8 2011 at 16:24:00 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2395 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 has a net charge of -0.0940 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: 1.752716 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): -2.480000 46.55700 ymin,ymax (A): -15.54100 29.74100 zmin,zma (A): -18.98200 41.95200 x,y,z range (A): 49.03700 45.28200 60.93400 scale (grids/A): 1.752716 object centre (A): 22.03850 7.100000 11.48500 number of atom coordinates read : 2395 total number of charged atoms : 2284 net assigned charge : 3.806002 assigned positive charge : 354.4140 centred at (gu) : 90.67802 86.14653 86.65720 assigned negative charge : -350.6088 centred at (gu) : 90.76128 86.55531 86.73197 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 57941 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19822 grid for indexing accessible points = 1.400000 m= 18406 mr = 40245 m= 2275 mr = 13214 m= 81 mr = 1304 m= 0 mr = 14 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 1913 time to turn everything in is 0.5400000 number of dielectric boundary points 23926 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 177 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 17795 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) : 0.5842387 object centre at (A) : 22.03850 7.100000 11.48500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9789597E-02 1.5978765E-02 midg,1,midg; midg,igrid,midg 1.4070023E-02 -2.9987490E-03 1,midg,midg; igrid,midg,midg 2.2424876E-03 -1.6435368E-02 gauss-seidel spectral radius is 0.9983602 estimated iterations to convergence 196 setup time was (sec) 0.8400000 now iterating at: 16:24:01 rms-change max change #iterations 3.376607 162.5196 at 10iterations 1.479675 64.51611 at 20iterations 0.6425669 23.50213 at 30iterations 0.2804348 10.95342 at 40iterations 0.1224131 4.793685 at 50iterations 5.3271279E-02 1.974286 at 60iterations 2.3211168E-02 0.8688812 at 70iterations 1.0109781E-02 0.3858719 at 80iterations 4.4303504E-03 0.1581078 at 90iterations 1.9444671E-03 7.5405121E-02 at 100iterations 8.5250003E-04 3.5461426E-02 at 110iterations 3.7666087E-04 1.5031815E-02 at 120iterations finished qdiffx linear iterations at : 16:24:09 total time elapsed so far: 8.960000 # loops : 120 mean,max change (kT/e) : 3.7666087E-04 1.5031815E-02 energy calculations done at 8.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.130000 DelPhi exited at 16:24:10 9.135u 0.275s 0:09.75 96.4% 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 Sat Oct 8 2011 at 16:24:10 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2395 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 has a net charge of -0.0940 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: 2.629074 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): -2.480000 46.55700 ymin,ymax (A): -15.54100 29.74100 zmin,zma (A): -18.98200 41.95200 x,y,z range (A): 49.03700 45.28200 60.93400 scale (grids/A): 2.629074 object centre (A): 22.03850 7.100000 11.48500 number of atom coordinates read : 2395 total number of charged atoms : 2284 net assigned charge : 3.806002 assigned positive charge : 354.4140 centred at (gu) : 91.01678 84.21965 84.98568 assigned negative charge : -350.6088 centred at (gu) : 91.14194 84.83292 85.09800 start vw surface at 0.1500000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 134474 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19822 grid for indexing accessible points = 1.400000 m= 62580 mr = 98046 m= 19618 mr = 50343 m= 3839 mr = 15526 m= 356 mr = 2757 m= 4 mr = 194 m= 0 mr = 0 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 6257 time to turn everything in is 1.280000 number of dielectric boundary points 54005 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.420000 number of grid points assigned charge 18261 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) : 1.752716 object centre at (A) : 22.03850 7.100000 11.48500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2382387 0.4789031 midg,1,midg; midg,igrid,midg 0.1572424 -4.3132804E-02 1,midg,midg; igrid,midg,midg 3.4082044E-02 -0.2876279 gauss-seidel spectral radius is 0.9991722 estimated iterations to convergence 274 setup time was (sec) 1.590000 now iterating at: 16:24:11 rms-change max change #iterations 8.396872 269.4904 at 10iterations 4.758163 136.8662 at 20iterations 2.689620 61.43011 at 30iterations 1.511185 33.63790 at 40iterations 0.8490320 18.90036 at 50iterations 0.4762545 10.93881 at 60iterations 0.2659257 5.965136 at 70iterations 0.1488142 3.503772 at 80iterations 8.3039656E-02 1.768442 at 90iterations 4.6378221E-02 1.002663 at 100iterations 2.5809027E-02 0.5381966 at 110iterations 1.4423506E-02 0.3047905 at 120iterations 8.0142180E-03 0.1752968 at 130iterations 4.4766897E-03 9.2864990E-02 at 140iterations 2.4943631E-03 5.0047874E-02 at 150iterations 1.3906304E-03 3.0906677E-02 at 160iterations 7.8031339E-04 1.7791748E-02 at 170iterations 4.3867869E-04 8.8634491E-03 at 180iterations finished qdiffx linear iterations at : 16:24:25 total time elapsed so far: 14.93000 # loops : 180 mean,max change (kT/e) : 4.3867869E-04 8.8634491E-03 energy calculations done at 14.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.11000 DelPhi exited at 16:24:25 15.112u 0.298s 0:15.86 97.0% 0+0k 0+0io 0pf+0w