Tue Apr 24 14:09:11 PDT 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.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 Tue Apr 24 2012 at 14:09:11 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 ! Automatically converted by prot2crg.py # of charge parameter records: 963 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4803 !!! WARNING: HIZ 293 has a net charge of 0.2000 !!! WARNING: HIZ 297 has a net charge of 0.2000 !!! WARNING: GLM 316 has a net charge of -0.8000 !!! WARNING: ASP 608 has a net charge of -2.0000 !!! WARNING: ZN1 901 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5392305 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): -19.41100 46.60900 ymin,ymax (A): 8.106000 73.11600 zmin,zma (A): 33.70100 95.40100 x,y,z range (A): 66.02000 65.00999 61.70000 scale (grids/A): 0.5392305 object centre (A): 13.59900 40.61100 64.55100 number of atom coordinates read : 4803 total number of charged atoms : 4644 net assigned charge : -0.9999646 assigned positive charge : 726.2723 centred at (gu) : 90.22601 90.97010 89.71324 assigned negative charge : -727.2772 centred at (gu) : 90.21551 90.93782 89.74872 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8786 nv = 96 ne = 84 npr = 99928 no. pairs analyzed = 99928 no. exposed pairs = 5781 no. arc points = 38798 no. surface atoms = 1947 nbur = 2856 mkacc time = 0.1700000 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 = 1.596000 m= 323 mr = 4810 m= 1 mr = 15 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 0.3300000 number of dielectric boundary points 4285 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3878 ## 474 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 11748 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6417227E-10 -3.2723191E-10 midg,1,midg; midg,igrid,midg -2.5440486E-10 2.8109226E-10 1,midg,midg; igrid,midg,midg -1.3270232E-10 3.8711690E-11 gauss-seidel spectral radius is 0.9823999 estimated iterations to convergence 62 setup time was (sec) 0.5400000 now iterating at: 14:09:12 rms-change max change #iterations 8.7179080E-02 11.52435 at 10iterations 5.9673325E-03 0.9801178 at 20iterations 6.9792365E-04 0.1176147 at 30iterations 2.3192885E-04 3.3792496E-02 at 40iterations 1.0156570E-04 1.4213204E-02 at 50iterations finished qdiffx linear iterations at : 14:09:16 total time elapsed so far: 3.630000 # loops : 50 mean,max change (kT/e) : 1.0156570E-04 1.4213204E-02 energy calculations done at 3.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.770000 DelPhi exited at 14:09:16 3.771u 0.203s 0:04.97 79.8% 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 Apr 24 2012 at 14:09:16 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 ! Automatically converted by prot2crg.py # of charge parameter records: 963 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4803 !!! WARNING: HIZ 293 has a net charge of 0.2000 !!! WARNING: HIZ 297 has a net charge of 0.2000 !!! WARNING: GLM 316 has a net charge of -0.8000 !!! WARNING: ASP 608 has a net charge of -2.0000 !!! WARNING: ZN1 901 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.617692 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): -19.41100 46.60900 ymin,ymax (A): 8.106000 73.11600 zmin,zma (A): 33.70100 95.40100 x,y,z range (A): 66.02000 65.00999 61.70000 scale (grids/A): 1.617692 object centre (A): 13.59900 40.61100 64.55100 number of atom coordinates read : 4803 total number of charged atoms : 4644 net assigned charge : -0.9999646 assigned positive charge : 726.2723 centred at (gu) : 90.67628 92.90885 89.13803 assigned negative charge : -727.2772 centred at (gu) : 90.64600 92.81297 89.24606 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 99209 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38798 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 31305 mr = 70489 m= 3283 mr = 21819 m= 90 mr = 1605 m= 0 mr = 9 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 860 time to turn everything in is 0.4800000 number of dielectric boundary points 39965 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 419 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 35504 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) : 0.5392305 object centre at (A) : 13.59900 40.61100 64.55100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.7584481E-03 6.3610617E-03 midg,1,midg; midg,igrid,midg -6.5298174E-03 -1.0224753E-02 1,midg,midg; igrid,midg,midg -3.3694681E-02 1.3802566E-03 gauss-seidel spectral radius is 0.9983253 estimated iterations to convergence 194 setup time was (sec) 0.7100000 now iterating at: 14:09:22 rms-change max change #iterations 4.298022 162.3420 at 10iterations 1.857978 62.63173 at 20iterations 0.8012217 23.39710 at 30iterations 0.3464989 12.01831 at 40iterations 0.1498079 4.416195 at 50iterations 6.4870350E-02 2.083682 at 60iterations 2.8153921E-02 0.8782406 at 70iterations 1.2258007E-02 0.3621085 at 80iterations 5.3994115E-03 0.1732330 at 90iterations 2.4377599E-03 7.7011108E-02 at 100iterations 1.1678853E-03 4.0406525E-02 at 110iterations 6.4247800E-04 2.1392345E-02 at 120iterations finished qdiffx linear iterations at : 14:09:30 total time elapsed so far: 8.410000 # loops : 120 mean,max change (kT/e) : 6.4247800E-04 2.1392345E-02 energy calculations done at 8.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.540000 DelPhi exited at 14:09:30 8.542u 0.308s 0:14.15 62.4% 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 Tue Apr 24 2012 at 14:09:31 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 ! Automatically converted by prot2crg.py # of charge parameter records: 963 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4803 !!! WARNING: HIZ 293 has a net charge of 0.2000 !!! WARNING: HIZ 297 has a net charge of 0.2000 !!! WARNING: GLM 316 has a net charge of -0.8000 !!! WARNING: ASP 608 has a net charge of -2.0000 !!! WARNING: ZN1 901 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.426537 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): -19.41100 46.60900 ymin,ymax (A): 8.106000 73.11600 zmin,zma (A): 33.70100 95.40100 x,y,z range (A): 66.02000 65.00999 61.70000 scale (grids/A): 2.426537 object centre (A): 13.59900 40.61100 64.55100 number of atom coordinates read : 4803 total number of charged atoms : 4644 net assigned charge : -0.9999646 assigned positive charge : 726.2723 centred at (gu) : 91.01389 94.36291 88.70671 assigned negative charge : -727.2772 centred at (gu) : 90.96893 94.21932 88.86880 start vw surface at 0.1300000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 231133 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38798 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 108418 mr = 172363 m= 31283 mr = 86559 m= 4994 mr = 23611 m= 358 mr = 3247 m= 8 mr = 167 m= 0 mr = 0 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 2883 time to turn everything in is 1.240000 number of dielectric boundary points 90247 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 24 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 37112 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) : 1.617692 object centre at (A) : 13.59900 40.61100 64.55100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.4358133E-02 0.1037777 midg,1,midg; midg,igrid,midg -0.1448976 -0.1430621 1,midg,midg; igrid,midg,midg -0.7297173 3.5356890E-02 gauss-seidel spectral radius is 0.9992204 estimated iterations to convergence 283 setup time was (sec) 1.510000 now iterating at: 14:09:38 rms-change max change #iterations 11.19765 281.1949 at 10iterations 6.542175 170.2919 at 20iterations 3.803363 83.25757 at 30iterations 2.200384 48.62911 at 40iterations 1.266574 24.93760 at 50iterations 0.7295172 14.21292 at 60iterations 0.4186288 9.232435 at 70iterations 0.2393139 4.213779 at 80iterations 0.1366487 2.728798 at 90iterations 7.8129292E-02 1.423039 at 100iterations 4.4600990E-02 0.9189832 at 110iterations 2.5387023E-02 0.4824829 at 120iterations 1.4519680E-02 0.2746663 at 130iterations 8.3182845E-03 0.1510925 at 140iterations 4.7918377E-03 8.4960938E-02 at 150iterations 2.8019850E-03 4.9039841E-02 at 160iterations 1.6825199E-03 3.1770706E-02 at 170iterations 1.0555737E-03 1.7517149E-02 at 180iterations finished qdiffx linear iterations at : 14:09:51 total time elapsed so far: 14.14000 # loops : 180 mean,max change (kT/e) : 1.0555737E-03 1.7517149E-02 energy calculations done at 14.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.28000 DelPhi exited at 14:09:52 14.279u 0.276s 0:21.20 68.5% 0+0k 0+0io 0pf+0w