Mon Oct 10 10:28:35 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+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 Mon Oct 10 2011 at 10:28:35 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2827 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: 0.5585365 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): -22.59400 41.14400 ymin,ymax (A): -12.28900 44.34000 zmin,zma (A): -1.947000 51.85900 x,y,z range (A): 63.73800 56.62900 53.80600 scale (grids/A): 0.5585365 object centre (A): 9.274999 16.02550 24.95600 number of atom coordinates read : 2827 total number of charged atoms : 2678 net assigned charge : 10.00003 assigned positive charge : 411.4209 centred at (gu) : 92.19225 91.43732 86.75813 assigned negative charge : -401.4214 centred at (gu) : 92.26601 91.45894 86.54906 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5918 nv = 96 ne = 84 npr = 55230 no. pairs analyzed = 55230 no. exposed pairs = 4186 no. arc points = 30488 no. surface atoms = 1391 nbur = 1436 mkacc time = 9.0000004E-02 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 = 1.540000 m= 246 mr = 2563 m= 0 mr = 9 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3592 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3008 ## 343 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7546 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.1435411E-09 1.3717739E-09 midg,1,midg; midg,igrid,midg 9.1096702E-10 1.2306172E-09 1,midg,midg; igrid,midg,midg 1.0443778E-09 6.2838357E-10 gauss-seidel spectral radius is 0.9834700 estimated iterations to convergence 64 setup time was (sec) 0.3900000 now iterating at: 10:28:35 rms-change max change #iterations 7.6023720E-02 13.95009 at 10iterations 5.4071634E-03 0.8160381 at 20iterations 3.9640261E-04 6.7607880E-02 at 30iterations 3.8121318E-05 6.6652298E-03 at 40iterations 6.0641887E-06 7.5769424E-04 at 50iterations finished qdiffx linear iterations at : 10:28:38 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 6.0641887E-06 7.5769424E-04 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 10:28:38 3.432u 0.185s 0:03.89 92.8% 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 Mon Oct 10 2011 at 10:28:39 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2827 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: 1.675610 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): -22.59400 41.14400 ymin,ymax (A): -12.28900 44.34000 zmin,zma (A): -1.947000 51.85900 x,y,z range (A): 63.73800 56.62900 53.80600 scale (grids/A): 1.675610 object centre (A): 9.274999 16.02550 24.95600 number of atom coordinates read : 2827 total number of charged atoms : 2678 net assigned charge : 10.00003 assigned positive charge : 411.4209 centred at (gu) : 96.57615 94.31160 80.27397 assigned negative charge : -401.4214 centred at (gu) : 96.79787 94.37658 79.64693 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 63767 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30488 grid for indexing accessible points = 1.400000 m= 19216 mr = 39001 m= 2089 mr = 12051 m= 63 mr = 890 m= 0 mr = 4 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 33189 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 281 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 20586 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) : 0.5585365 object centre at (A) : 9.274999 16.02550 24.95600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.4468686E-03 1.1580234E-02 midg,1,midg; midg,igrid,midg 1.5864950E-02 2.2841176E-02 1,midg,midg; igrid,midg,midg -9.7811231E-03 -1.1807621E-02 gauss-seidel spectral radius is 0.9982718 estimated iterations to convergence 191 setup time was (sec) 0.5300000 now iterating at: 10:28:39 rms-change max change #iterations 3.304369 141.6783 at 10iterations 1.399270 59.90170 at 20iterations 0.5910540 22.49191 at 30iterations 0.2514200 9.773618 at 40iterations 0.1064747 3.936285 at 50iterations 4.5068737E-02 1.732986 at 60iterations 1.9115340E-02 0.7377415 at 70iterations 8.1377551E-03 0.3062935 at 80iterations 3.4595483E-03 0.1255569 at 90iterations 1.4700445E-03 5.6974411E-02 at 100iterations 6.2344311E-04 2.2307634E-02 at 110iterations 2.6745905E-04 9.1047287E-03 at 120iterations finished qdiffx linear iterations at : 10:28:46 total time elapsed so far: 7.670000 # loops : 120 mean,max change (kT/e) : 2.6745905E-04 9.1047287E-03 energy calculations done at 7.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.820000 DelPhi exited at 10:28:47 7.822u 0.209s 0:08.37 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 Mon Oct 10 2011 at 10:28:47 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2827 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: 2.513414 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): -22.59400 41.14400 ymin,ymax (A): -12.28900 44.34000 zmin,zma (A): -1.947000 51.85900 x,y,z range (A): 63.73800 56.62900 53.80600 scale (grids/A): 2.513414 object centre (A): 9.274999 16.02550 24.95600 number of atom coordinates read : 2827 total number of charged atoms : 2678 net assigned charge : 10.00003 assigned positive charge : 411.4209 centred at (gu) : 99.86421 96.46729 75.41088 assigned negative charge : -401.4214 centred at (gu) : 100.1968 96.56484 74.47036 start vw surface at 0.1000000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 147543 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30488 grid for indexing accessible points = 1.400000 m= 64652 mr = 96425 m= 19075 mr = 48071 m= 3191 mr = 13424 m= 238 mr = 1843 m= 6 mr = 98 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8000000 number of dielectric boundary points 74844 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 21416 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) : 1.675610 object centre at (A) : 9.274999 16.02550 24.95600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3132087E-03 0.1330130 midg,1,midg; midg,igrid,midg 0.3054167 0.2800254 1,midg,midg; igrid,midg,midg -0.3320747 -0.3695213 gauss-seidel spectral radius is 0.9991674 estimated iterations to convergence 274 setup time was (sec) 1.040000 now iterating at: 10:28:48 rms-change max change #iterations 8.807585 348.9537 at 10iterations 5.125129 179.5848 at 20iterations 2.930235 87.37051 at 30iterations 1.662200 48.74365 at 40iterations 0.9391162 30.96655 at 50iterations 0.5286224 13.52462 at 60iterations 0.2965549 7.704739 at 70iterations 0.1663439 4.221596 at 80iterations 9.2834048E-02 2.157417 at 90iterations 5.1781196E-02 1.416800 at 100iterations 2.8805783E-02 0.7087555 at 110iterations 1.6077586E-02 0.3487594 at 120iterations 8.9496858E-03 0.1923904 at 130iterations 4.9793450E-03 0.1167707 at 140iterations 2.7682364E-03 6.8756104E-02 at 150iterations 1.5400434E-03 3.6885262E-02 at 160iterations 8.5524062E-04 1.9248962E-02 at 170iterations 4.7565592E-04 9.5770359E-03 at 180iterations finished qdiffx linear iterations at : 10:28:59 total time elapsed so far: 12.31000 # loops : 180 mean,max change (kT/e) : 4.7565592E-04 9.5770359E-03 energy calculations done at 12.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.44000 DelPhi exited at 10:29:00 12.444u 0.181s 0:12.96 97.3% 0+0k 0+0io 0pf+0w