Sun Oct 9 11:16:52 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 Sun Oct 9 2011 at 11:16:52 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2872 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: 0.5805799 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): -22.60600 38.71200 ymin,ymax (A): -26.13100 30.48000 zmin,zma (A): -30.92200 26.13300 x,y,z range (A): 61.31800 56.61100 57.05500 scale (grids/A): 0.5805799 object centre (A): 8.053000 2.174500 -2.394501 number of atom coordinates read : 2872 total number of charged atoms : 2781 net assigned charge : 6.000010 assigned positive charge : 427.0461 centred at (gu) : 89.51347 89.19147 91.86301 assigned negative charge : -421.0478 centred at (gu) : 89.56853 89.16392 91.82584 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6697 nv = 96 ne = 84 npr = 55021 no. pairs analyzed = 55021 no. exposed pairs = 4080 no. arc points = 28734 no. surface atoms = 1357 nbur = 1515 mkacc time = 0.1600000 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 = 1.484000 m= 367 mr = 3265 m= 0 mr = 43 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3756 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2880 ## 271 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8457 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.5677794E-10 3.2389631E-09 midg,1,midg; midg,igrid,midg 8.6953567E-10 1.5749639E-09 1,midg,midg; igrid,midg,midg 2.7673159E-09 1.3293380E-10 gauss-seidel spectral radius is 0.9846943 estimated iterations to convergence 66 setup time was (sec) 0.6200000 now iterating at: 11:16:53 rms-change max change #iterations 9.3023010E-02 13.28234 at 10iterations 7.3989118E-03 1.171976 at 20iterations 7.8205019E-04 0.1150627 at 30iterations 1.4498654E-04 2.4410248E-02 at 40iterations 3.5732988E-05 6.1416626E-03 at 50iterations finished qdiffx linear iterations at : 11:16:57 total time elapsed so far: 3.890000 # loops : 50 mean,max change (kT/e) : 3.5732988E-05 6.1416626E-03 energy calculations done at 3.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.060000 DelPhi exited at 11:16:57 4.067u 0.289s 0:04.97 87.3% 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 Sun Oct 9 2011 at 11:16:57 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 = 2872 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: 1.741740 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): -22.60600 38.71200 ymin,ymax (A): -26.13100 30.48000 zmin,zma (A): -30.92200 26.13300 x,y,z range (A): 61.31800 56.61100 57.05500 scale (grids/A): 1.741740 object centre (A): 8.053000 2.174500 -2.394501 number of atom coordinates read : 2872 total number of charged atoms : 2781 net assigned charge : 6.000010 assigned positive charge : 427.0461 centred at (gu) : 88.53958 87.57381 95.58826 assigned negative charge : -421.0478 centred at (gu) : 88.70544 87.49145 95.47727 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 73176 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28734 grid for indexing accessible points = 1.400000 m= 24153 mr = 48162 m= 3513 mr = 16236 m= 161 mr = 1944 m= 2 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6500000 number of dielectric boundary points 34631 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 186 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 21596 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) : 0.5805799 object centre at (A) : 8.053000 2.174500 -2.394501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3685304E-03 1.2585393E-02 midg,1,midg; midg,igrid,midg 1.9188622E-02 1.7524343E-02 1,midg,midg; igrid,midg,midg 1.6513709E-02 -1.4175245E-02 gauss-seidel spectral radius is 0.9984273 estimated iterations to convergence 200 setup time was (sec) 0.9600000 now iterating at: 11:16:59 rms-change max change #iterations 3.714077 211.0559 at 10iterations 1.629129 57.85079 at 20iterations 0.7175812 26.87235 at 30iterations 0.3160368 13.05869 at 40iterations 0.1408614 4.682655 at 50iterations 6.2118452E-02 2.289920 at 60iterations 2.7495984E-02 0.9160500 at 70iterations 1.2216599E-02 0.4478607 at 80iterations 5.4359939E-03 0.1921921 at 90iterations 2.4341019E-03 8.4014893E-02 at 100iterations 1.0998589E-03 4.4624329E-02 at 110iterations 5.0424720E-04 1.8695831E-02 at 120iterations finished qdiffx linear iterations at : 11:17:07 total time elapsed so far: 9.220000 # loops : 120 mean,max change (kT/e) : 5.0424720E-04 1.8695831E-02 energy calculations done at 9.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.380000 DelPhi exited at 11:17:07 9.387u 0.299s 0:09.95 97.1% 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 11:17:07 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 = 2872 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: 2.612610 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): -22.60600 38.71200 ymin,ymax (A): -26.13100 30.48000 zmin,zma (A): -30.92200 26.13300 x,y,z range (A): 61.31800 56.61100 57.05500 scale (grids/A): 2.612610 object centre (A): 8.053000 2.174500 -2.394501 number of atom coordinates read : 2872 total number of charged atoms : 2781 net assigned charge : 6.000010 assigned positive charge : 427.0461 centred at (gu) : 87.80914 86.36035 98.38219 assigned negative charge : -421.0478 centred at (gu) : 88.05815 86.23718 98.21599 start vw surface at 0.1600000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 169754 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28734 grid for indexing accessible points = 1.400000 m= 79492 mr = 118400 m= 26692 mr = 61343 m= 5942 mr = 19987 m= 623 mr = 4156 m= 8 mr = 328 m= 0 mr = 0 time to grow re-entrant surface = 0.9900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.630000 number of dielectric boundary points 78297 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.790000 number of grid points assigned charge 22230 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) : 1.741740 object centre at (A) : 8.053000 2.174500 -2.394501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.8093707E-04 0.2018904 midg,1,midg; midg,igrid,midg 0.3858957 0.2360691 1,midg,midg; igrid,midg,midg 0.2417737 -0.2580518 gauss-seidel spectral radius is 0.9992197 estimated iterations to convergence 283 setup time was (sec) 1.960000 now iterating at: 11:17:10 rms-change max change #iterations 9.389163 287.4373 at 10iterations 5.522722 169.5898 at 20iterations 3.210912 65.14232 at 30iterations 1.854749 36.70264 at 40iterations 1.071508 23.76285 at 50iterations 0.6140379 12.76448 at 60iterations 0.3511621 7.292250 at 70iterations 0.2001190 4.015245 at 80iterations 0.1137669 2.179646 at 90iterations 6.4742930E-02 1.260231 at 100iterations 3.6833238E-02 0.6540270 at 110iterations 2.0895956E-02 0.3930550 at 120iterations 1.1884063E-02 0.2441759 at 130iterations 6.7562577E-03 0.1396561 at 140iterations 3.8418551E-03 7.1128845E-02 at 150iterations 2.1889571E-03 4.5631409E-02 at 160iterations 1.2514009E-03 2.3995161E-02 at 170iterations 7.2176824E-04 1.3751984E-02 at 180iterations finished qdiffx linear iterations at : 11:17:23 total time elapsed so far: 15.61000 # loops : 180 mean,max change (kT/e) : 7.2176824E-04 1.3751984E-02 energy calculations done at 15.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.79000 DelPhi exited at 11:17:24 15.796u 0.306s 0:16.39 98.1% 0+0k 0+0io 0pf+0w