Tue Oct 11 06:12:13 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 06:12:13 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2065 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 0.7210711 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): 3.604000 46.46400 ymin,ymax (A): 0.6409999 41.44200 zmin,zma (A): -2.097000 47.27400 x,y,z range (A): 42.86000 40.80100 49.37100 scale (grids/A): 0.7210711 object centre (A): 25.03400 21.04150 22.58850 number of atom coordinates read : 2065 total number of charged atoms : 1933 net assigned charge : 6.550011 assigned positive charge : 313.4571 centred at (gu) : 90.30079 90.26403 90.30672 assigned negative charge : -306.9071 centred at (gu) : 90.50341 90.24243 90.34521 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7403 nv = 96 ne = 84 npr = 41405 no. pairs analyzed = 41405 no. exposed pairs = 2509 no. arc points = 17167 no. surface atoms = 852 nbur = 1213 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 531 mr = 4331 m= 5 mr = 85 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3523 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1594 ## 131 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 7994 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.5950298E-08 5.4041298E-08 midg,1,midg; midg,igrid,midg 5.9375104E-08 9.5192341E-08 1,midg,midg; igrid,midg,midg 1.9513575E-07 -6.2935612E-08 gauss-seidel spectral radius is 0.9899693 estimated iterations to convergence 81 setup time was (sec) 0.4700000 now iterating at: 06:12:14 rms-change max change #iterations 0.2143413 27.47064 at 10iterations 2.8979585E-02 4.240593 at 20iterations 4.1688988E-03 0.5845680 at 30iterations 8.2790956E-04 9.9395752E-02 at 40iterations 2.4490553E-04 3.1398773E-02 at 50iterations finished qdiffx linear iterations at : 06:12:17 total time elapsed so far: 3.040000 # loops : 50 mean,max change (kT/e) : 2.4490553E-04 3.1398773E-02 energy calculations done at 3.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.220000 DelPhi exited at 06:12:17 3.224u 0.215s 0:04.10 83.6% 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 Tue Oct 11 2011 at 06:12:17 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2065 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 2.163213 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): 3.604000 46.46400 ymin,ymax (A): 0.6409999 41.44200 zmin,zma (A): -2.097000 47.27400 x,y,z range (A): 42.86000 40.80100 49.37100 scale (grids/A): 2.163213 object centre (A): 25.03400 21.04150 22.58850 number of atom coordinates read : 2065 total number of charged atoms : 1933 net assigned charge : 6.550011 assigned positive charge : 313.4571 centred at (gu) : 90.90241 90.79228 90.92015 assigned negative charge : -306.9071 centred at (gu) : 91.51051 90.72743 91.03551 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 78262 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17167 grid for indexing accessible points = 1.400000 m= 32288 mr = 56087 m= 6358 mr = 24695 m= 569 mr = 4235 m= 15 mr = 267 m= 0 mr = 3 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 32205 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 49 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 15337 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) : 0.7210711 object centre at (A) : 25.03400 21.04150 22.58850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.0321748E-02 6.0216941E-02 midg,1,midg; midg,igrid,midg 2.6200840E-03 3.1659033E-02 1,midg,midg; igrid,midg,midg 4.9158871E-02 -9.0988632E-03 gauss-seidel spectral radius is 0.9988672 estimated iterations to convergence 235 setup time was (sec) 0.8800000 now iterating at: 06:12:19 rms-change max change #iterations 4.762609 205.2614 at 10iterations 2.388119 84.04238 at 20iterations 1.203141 36.23001 at 30iterations 0.6033279 18.22758 at 40iterations 0.3036607 9.348057 at 50iterations 0.1527607 5.347626 at 60iterations 7.6601431E-02 2.180664 at 70iterations 3.8850710E-02 1.158766 at 80iterations 1.9697811E-02 0.5862978 at 90iterations 1.0116027E-02 0.3081894 at 100iterations 5.2274489E-03 0.1553946 at 110iterations 2.8057764E-03 8.5117340E-02 at 120iterations finished qdiffx linear iterations at : 06:12:25 total time elapsed so far: 7.260000 # loops : 120 mean,max change (kT/e) : 2.8057764E-03 8.5117340E-02 energy calculations done at 7.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.440000 DelPhi exited at 06:12:25 7.440u 0.198s 0:08.00 95.3% 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 06:12:26 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2065 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 3.244820 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): 3.604000 46.46400 ymin,ymax (A): 0.6409999 41.44200 zmin,zma (A): -2.097000 47.27400 x,y,z range (A): 42.86000 40.80100 49.37100 scale (grids/A): 3.244820 object centre (A): 25.03400 21.04150 22.58850 number of atom coordinates read : 2065 total number of charged atoms : 1933 net assigned charge : 6.550011 assigned positive charge : 313.4571 centred at (gu) : 91.35369 91.18841 91.38026 assigned negative charge : -306.9071 centred at (gu) : 92.26579 91.09106 91.55325 start vw surface at 0.1300000 fill in re-entrant regions at 0.8100000 boundary points on vw surface= 180292 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17167 grid for indexing accessible points = 1.400000 m= 100068 mr = 134794 m= 41345 mr = 83568 m= 12075 mr = 34322 m= 2363 mr = 9372 m= 240 mr = 1651 m= 11 mr = 142 m= 0 mr = 4 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.820000 number of dielectric boundary points 72541 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.960000 number of grid points assigned charge 15464 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) : 2.163213 object centre at (A) : 25.03400 21.04150 22.58850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5069997 0.6197774 midg,1,midg; midg,igrid,midg -3.0948779E-02 0.2373864 1,midg,midg; igrid,midg,midg 0.3544521 1.9716894E-02 gauss-seidel spectral radius is 0.9993035 estimated iterations to convergence 299 setup time was (sec) 2.130000 now iterating at: 06:12:28 rms-change max change #iterations 10.48827 351.6407 at 10iterations 6.227798 143.8149 at 20iterations 3.682379 70.07574 at 30iterations 2.177943 41.44327 at 40iterations 1.285979 22.63205 at 50iterations 0.7576647 15.42023 at 60iterations 0.4467357 8.079639 at 70iterations 0.2624593 4.539933 at 80iterations 0.1546757 2.682111 at 90iterations 9.1059536E-02 1.552889 at 100iterations 5.3674851E-02 0.9878540 at 110iterations 3.1809695E-02 0.5326309 at 120iterations 1.9017948E-02 0.3162365 at 130iterations 1.1601676E-02 0.2022400 at 140iterations 7.3074885E-03 0.1376629 at 150iterations 4.8207240E-03 8.1876755E-02 at 160iterations 3.3840814E-03 5.8235168E-02 at 170iterations 2.5299166E-03 4.0279388E-02 at 180iterations finished qdiffx linear iterations at : 06:12:38 total time elapsed so far: 12.32000 # loops : 180 mean,max change (kT/e) : 2.5299166E-03 4.0279388E-02 energy calculations done at 12.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.49000 DelPhi exited at 06:12:39 12.495u 0.236s 0:13.37 95.1% 0+0k 0+0io 0pf+0w