Sun Oct 9 07:36:40 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 Sun Oct 9 2011 at 07:36:40 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1698 !!! WARNING: MN1 160 has a net charge of 1.4000 !!! WARNING: NAP 161 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7190176 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): 5.905000 49.05100 ymin,ymax (A): 20.48200 69.99400 zmin,zma (A): -6.165000 34.81900 x,y,z range (A): 43.14600 49.51200 40.98400 scale (grids/A): 0.7190176 object centre (A): 27.47800 45.23800 14.32700 number of atom coordinates read : 1698 total number of charged atoms : 1561 net assigned charge : -10.09999 assigned positive charge : 253.2242 centred at (gu) : 90.04163 89.50007 89.34800 assigned negative charge : -263.3241 centred at (gu) : 90.13599 89.41360 89.64834 start vw surface at 5.9999999E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 6017 nv = 96 ne = 84 npr = 36476 no. pairs analyzed = 36476 no. exposed pairs = 2090 no. arc points = 14804 no. surface atoms = 707 nbur = 991 mkacc time = 5.9999995E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 370 mr = 3409 m= 3 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 7.0000000E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1400000 number of dielectric boundary points 2908 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1257 ## 88 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 6451 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.1956341E-08 -2.4587567E-07 midg,1,midg; midg,igrid,midg -1.7480488E-07 -6.0391045E-08 1,midg,midg; igrid,midg,midg -6.1338902E-08 -1.6463895E-07 gauss-seidel spectral radius is 0.9898813 estimated iterations to convergence 81 setup time was (sec) 0.3400000 now iterating at: 07:36:40 rms-change max change #iterations 0.1973979 31.22710 at 10iterations 2.5097253E-02 3.807167 at 20iterations 3.1540040E-03 0.4929142 at 30iterations 3.9916043E-04 6.4572811E-02 at 40iterations 4.9667757E-05 6.6442490E-03 at 50iterations finished qdiffx linear iterations at : 07:36:43 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 4.9667757E-05 6.6442490E-03 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 07:36:44 3.305u 0.160s 0:03.73 92.7% 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 Sun Oct 9 2011 at 07:36:44 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1698 !!! WARNING: MN1 160 has a net charge of 1.4000 !!! WARNING: NAP 161 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.157053 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): 5.905000 49.05100 ymin,ymax (A): 20.48200 69.99400 zmin,zma (A): -6.165000 34.81900 x,y,z range (A): 43.14600 49.51200 40.98400 scale (grids/A): 2.157053 object centre (A): 27.47800 45.23800 14.32700 number of atom coordinates read : 1698 total number of charged atoms : 1561 net assigned charge : -10.09999 assigned positive charge : 253.2242 centred at (gu) : 90.12499 88.50047 88.04401 assigned negative charge : -263.3241 centred at (gu) : 90.40798 88.24079 88.94492 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 62826 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14804 grid for indexing accessible points = 1.400000 m= 25219 mr = 43510 m= 4934 mr = 19585 m= 392 mr = 3455 m= 6 mr = 201 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 26626 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 31 iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 12428 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) : 0.7190176 object centre at (A) : 27.47800 45.23800 14.32700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4243386E-02 -6.8689577E-02 midg,1,midg; midg,igrid,midg -7.0918895E-02 -1.0311992E-02 1,midg,midg; igrid,midg,midg -3.0594379E-02 -5.7918590E-02 gauss-seidel spectral radius is 0.9988288 estimated iterations to convergence 231 setup time was (sec) 0.5400000 now iterating at: 07:36:44 rms-change max change #iterations 4.382828 208.1057 at 10iterations 2.163298 85.30465 at 20iterations 1.069675 36.88174 at 30iterations 0.5285894 16.19231 at 40iterations 0.2609435 8.451637 at 50iterations 0.1293782 4.700190 at 60iterations 6.4167514E-02 2.011831 at 70iterations 3.1740744E-02 0.9806252 at 80iterations 1.5675940E-02 0.4924698 at 90iterations 7.7817044E-03 0.2501812 at 100iterations 3.8443170E-03 0.1430092 at 110iterations 1.9083288E-03 5.7900906E-02 at 120iterations finished qdiffx linear iterations at : 07:36:51 total time elapsed so far: 7.460000 # loops : 120 mean,max change (kT/e) : 1.9083288E-03 5.7900906E-02 energy calculations done at 7.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.600000 DelPhi exited at 07:36:52 7.603u 0.184s 0:08.06 96.5% 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 Sun Oct 9 2011 at 07:36:52 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1698 !!! WARNING: MN1 160 has a net charge of 1.4000 !!! WARNING: NAP 161 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.235579 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): 5.905000 49.05100 ymin,ymax (A): 20.48200 69.99400 zmin,zma (A): -6.165000 34.81900 x,y,z range (A): 43.14600 49.51200 40.98400 scale (grids/A): 3.235579 object centre (A): 27.47800 45.23800 14.32700 number of atom coordinates read : 1698 total number of charged atoms : 1561 net assigned charge : -10.09999 assigned positive charge : 253.2242 centred at (gu) : 90.18752 87.75069 87.06600 assigned negative charge : -263.3241 centred at (gu) : 90.61206 87.36117 88.41744 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 144878 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14804 grid for indexing accessible points = 1.400000 m= 77311 mr = 104826 m= 33000 mr = 64773 m= 9578 mr = 27866 m= 1648 mr = 7683 m= 153 mr = 1255 m= 2 mr = 97 m= 0 mr = 0 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9800000 number of dielectric boundary points 60070 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.060000 number of grid points assigned charge 12488 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) : 2.157053 object centre at (A) : 27.47800 45.23800 14.32700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2949960 -0.4699497 midg,1,midg; midg,igrid,midg -0.5937446 -8.4766010E-03 1,midg,midg; igrid,midg,midg -0.1816843 -0.4118244 gauss-seidel spectral radius is 0.9992862 estimated iterations to convergence 295 setup time was (sec) 1.200000 now iterating at: 07:36:53 rms-change max change #iterations 9.643337 382.9839 at 10iterations 5.544307 123.6163 at 20iterations 3.209967 71.73597 at 30iterations 1.858821 41.08317 at 40iterations 1.077617 19.87148 at 50iterations 0.6232966 11.90862 at 60iterations 0.3608731 6.243543 at 70iterations 0.2089776 3.698448 at 80iterations 0.1209994 2.265100 at 90iterations 6.9926210E-02 1.377136 at 100iterations 4.0537190E-02 0.8098717 at 110iterations 2.3495523E-02 0.4326973 at 120iterations 1.3589112E-02 0.2627783 at 130iterations 7.8983884E-03 0.1484909 at 140iterations 4.5691775E-03 9.1749191E-02 at 150iterations 2.6380050E-03 4.7916412E-02 at 160iterations 1.5311074E-03 2.6905060E-02 at 170iterations 8.8634348E-04 1.6559601E-02 at 180iterations finished qdiffx linear iterations at : 07:37:04 total time elapsed so far: 12.12000 # loops : 180 mean,max change (kT/e) : 8.8634348E-04 1.6559601E-02 energy calculations done at 12.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.25000 DelPhi exited at 07:37:05 12.254u 0.194s 0:12.74 97.6% 0+0k 0+0io 0pf+0w