Sat Oct 8 19:45:17 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 Sat Oct 8 2011 at 19:45:17 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 643 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6200038 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): -31.24900 17.62900 ymin,ymax (A): -23.60700 23.03700 zmin,zma (A): -12.37000 45.04900 x,y,z range (A): 48.87800 46.64400 57.41900 scale (grids/A): 0.6200038 object centre (A): -6.810000 -0.2850008 16.33950 number of atom coordinates read : 2606 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 88.48356 89.17747 89.54363 assigned negative charge : -388.8955 centred at (gu) : 88.36930 89.22713 89.41848 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6447 nv = 96 ne = 84 npr = 54873 no. pairs analyzed = 54873 no. exposed pairs = 3014 no. arc points = 21684 no. surface atoms = 1011 nbur = 1595 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 313 mr = 3563 m= 2 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 96 time to turn everything in is 0.2100000 number of dielectric boundary points 3161 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2229 ## 237 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8100 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.1870281E-09 1.0811354E-08 midg,1,midg; midg,igrid,midg 8.4356593E-09 4.0352510E-10 1,midg,midg; igrid,midg,midg -5.6195479E-09 8.0758591E-09 gauss-seidel spectral radius is 0.9865230 estimated iterations to convergence 71 setup time was (sec) 0.4200000 now iterating at: 19:45:17 rms-change max change #iterations 0.1270301 17.97659 at 10iterations 1.1644728E-02 1.915341 at 20iterations 1.0817670E-03 0.1571503 at 30iterations 1.0205514E-04 1.5441895E-02 at 40iterations 1.0138021E-05 1.8043518E-03 at 50iterations finished qdiffx linear iterations at : 19:45:21 total time elapsed so far: 3.570000 # loops : 50 mean,max change (kT/e) : 1.0138021E-05 1.8043518E-03 energy calculations done at 3.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.700000 DelPhi exited at 19:45:21 3.705u 0.214s 0:04.22 92.6% 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 Sat Oct 8 2011 at 19:45:21 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 643 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.860012 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): -31.24900 17.62900 ymin,ymax (A): -23.60700 23.03700 zmin,zma (A): -12.37000 45.04900 x,y,z range (A): 48.87800 46.64400 57.41900 scale (grids/A): 1.860012 object centre (A): -6.810000 -0.2850008 16.33950 number of atom coordinates read : 2606 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 85.45003 87.53223 88.63068 assigned negative charge : -388.8955 centred at (gu) : 85.10762 87.68114 88.25521 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 70137 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21684 grid for indexing accessible points = 1.400000 m= 23973 mr = 48950 m= 3292 mr = 17478 m= 167 mr = 1981 m= 2 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 4173 time to turn everything in is 0.3600000 number of dielectric boundary points 29105 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 178 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 19349 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) : 0.6200038 object centre at (A) : -6.810000 -0.2850008 16.33950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3732880E-02 2.9097855E-02 midg,1,midg; midg,igrid,midg 1.0567465E-02 8.8864187E-04 1,midg,midg; igrid,midg,midg -1.0707161E-03 4.0200934E-02 gauss-seidel spectral radius is 0.9985642 estimated iterations to convergence 209 setup time was (sec) 0.6100000 now iterating at: 19:45:22 rms-change max change #iterations 4.020408 168.8170 at 10iterations 1.852742 63.26951 at 20iterations 0.8472927 29.48692 at 30iterations 0.3896410 12.53834 at 40iterations 0.1790937 6.242650 at 50iterations 8.2163990E-02 2.882478 at 60iterations 3.7850052E-02 1.224937 at 70iterations 1.7377112E-02 0.6348858 at 80iterations 7.9857586E-03 0.2544327 at 90iterations 3.6626963E-03 0.1259623 at 100iterations 1.6879383E-03 5.4824829E-02 at 110iterations 7.7872403E-04 2.7057171E-02 at 120iterations finished qdiffx linear iterations at : 19:45:30 total time elapsed so far: 8.320000 # loops : 120 mean,max change (kT/e) : 7.7872403E-04 2.7057171E-02 energy calculations done at 8.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.450000 DelPhi exited at 19:45:30 8.456u 0.248s 0:09.01 96.4% 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 Sat Oct 8 2011 at 19:45:30 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 643 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.790017 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): -31.24900 17.62900 ymin,ymax (A): -23.60700 23.03700 zmin,zma (A): -12.37000 45.04900 x,y,z range (A): 48.87800 46.64400 57.41900 scale (grids/A): 2.790017 object centre (A): -6.810000 -0.2850008 16.33950 number of atom coordinates read : 2606 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 83.17487 86.29810 87.94588 assigned negative charge : -388.8955 centred at (gu) : 82.66142 86.52173 87.38284 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 162442 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21684 grid for indexing accessible points = 1.400000 m= 79446 mr = 118458 m= 26597 mr = 65175 m= 5711 mr = 21084 m= 697 mr = 4216 m= 41 mr = 450 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 14154 time to turn everything in is 0.9000000 number of dielectric boundary points 65533 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 19727 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) : 1.860012 object centre at (A) : -6.810000 -0.2850008 16.33950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1691633 0.3591821 midg,1,midg; midg,igrid,midg 0.1359462 -7.7909338E-03 1,midg,midg; igrid,midg,midg -2.6716292E-02 0.5061609 gauss-seidel spectral radius is 0.9992318 estimated iterations to convergence 285 setup time was (sec) 1.160000 now iterating at: 19:45:31 rms-change max change #iterations 9.488346 339.8865 at 10iterations 5.452708 129.0180 at 20iterations 3.117063 69.16378 at 30iterations 1.778632 41.23279 at 40iterations 1.014342 19.24620 at 50iterations 0.5774377 13.79188 at 60iterations 0.3290561 7.000690 at 70iterations 0.1868626 3.772797 at 80iterations 0.1063615 2.009546 at 90iterations 6.0604148E-02 1.284796 at 100iterations 3.4463730E-02 0.7254858 at 110iterations 1.9594628E-02 0.3534021 at 120iterations 1.1116983E-02 0.2343254 at 130iterations 6.3246447E-03 0.1141586 at 140iterations 3.5976530E-03 7.2727203E-02 at 150iterations 2.0444121E-03 3.8561821E-02 at 160iterations 1.1648475E-03 2.3056030E-02 at 170iterations 6.6448963E-04 1.3442993E-02 at 180iterations finished qdiffx linear iterations at : 19:45:44 total time elapsed so far: 13.34000 # loops : 180 mean,max change (kT/e) : 6.6448963E-04 1.3442993E-02 energy calculations done at 13.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.47000 DelPhi exited at 19:45:44 13.470u 0.250s 0:13.98 98.1% 0+0k 0+0io 0pf+0w