Sat Oct 15 13:12:42 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 Sat Oct 15 2011 at 13:12:42 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: 350 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2620 !!! WARNING: HIR 108 has a net charge of 0.5140 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: 0.5934520 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): -36.21300 12.09200 ymin,ymax (A): 31.29700 91.28500 zmin,zma (A): -24.51200 33.36500 x,y,z range (A): 48.30500 59.98801 57.87700 scale (grids/A): 0.5934520 object centre (A): -12.06050 61.29100 4.426499 number of atom coordinates read : 2620 total number of charged atoms : 2481 net assigned charge : 2.014009 assigned positive charge : 410.5027 centred at (gu) : 90.38942 88.15331 87.87295 assigned negative charge : -408.4894 centred at (gu) : 90.50818 88.03510 87.73623 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6221 nv = 96 ne = 84 npr = 50819 no. pairs analyzed = 50819 no. exposed pairs = 3615 no. arc points = 24792 no. surface atoms = 1211 nbur = 1409 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 266 mr = 3094 m= 2 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3385 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2450 ## 263 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7685 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.6688707E-09 3.1062020E-09 midg,1,midg; midg,igrid,midg -4.3839936E-09 2.9466918E-09 1,midg,midg; igrid,midg,midg 4.1252370E-09 -3.1094589E-09 gauss-seidel spectral radius is 0.9853163 estimated iterations to convergence 68 setup time was (sec) 0.4200000 now iterating at: 13:12:43 rms-change max change #iterations 0.1049129 16.92041 at 10iterations 8.6367978E-03 1.529163 at 20iterations 7.0709636E-04 0.1072845 at 30iterations 6.0097427E-05 9.1171265E-03 at 40iterations 6.0257053E-06 1.0223389E-03 at 50iterations finished qdiffx linear iterations at : 13:12:46 total time elapsed so far: 3.700000 # loops : 50 mean,max change (kT/e) : 6.0257053E-06 1.0223389E-03 energy calculations done at 3.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.830000 DelPhi exited at 13:12:47 3.838u 0.220s 0:04.32 93.7% 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 Sat Oct 15 2011 at 13:12:47 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: 350 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2620 !!! WARNING: HIR 108 has a net charge of 0.5140 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: 1.780356 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): -36.21300 12.09200 ymin,ymax (A): 31.29700 91.28500 zmin,zma (A): -24.51200 33.36500 x,y,z range (A): 48.30500 59.98801 57.87700 scale (grids/A): 1.780356 object centre (A): -12.06050 61.29100 4.426499 number of atom coordinates read : 2620 total number of charged atoms : 2481 net assigned charge : 2.014009 assigned positive charge : 410.5027 centred at (gu) : 91.16779 84.45934 83.61797 assigned negative charge : -408.4894 centred at (gu) : 91.52424 84.10502 83.20832 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 68212 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24792 grid for indexing accessible points = 1.400000 m= 21140 mr = 45029 m= 2299 mr = 14224 m= 85 mr = 1104 m= 0 mr = 6 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 31373 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 227 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 19331 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) : 0.5934520 object centre at (A) : -12.06050 61.29100 4.426499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2818819E-03 7.0968871E-03 midg,1,midg; midg,igrid,midg -4.3664757E-02 2.2510447E-02 1,midg,midg; igrid,midg,midg 1.3896419E-02 -1.3703652E-02 gauss-seidel spectral radius is 0.9984393 estimated iterations to convergence 201 setup time was (sec) 0.6100000 now iterating at: 13:12:48 rms-change max change #iterations 3.864714 168.9132 at 10iterations 1.703326 59.37400 at 20iterations 0.7547593 27.09918 at 30iterations 0.3330180 11.43657 at 40iterations 0.1478165 5.245333 at 50iterations 6.5685250E-02 2.268051 at 60iterations 2.9209647E-02 1.021721 at 70iterations 1.2936421E-02 0.4317513 at 80iterations 5.7485318E-03 0.2084217 at 90iterations 2.5550381E-03 8.9232564E-02 at 100iterations 1.1365111E-03 4.3188095E-02 at 110iterations 5.0806906E-04 1.6157150E-02 at 120iterations finished qdiffx linear iterations at : 13:12:56 total time elapsed so far: 8.690000 # loops : 120 mean,max change (kT/e) : 5.0806906E-04 1.6157150E-02 energy calculations done at 8.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.830000 DelPhi exited at 13:12:57 8.831u 0.279s 0:09.74 93.4% 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 15 2011 at 13:12:57 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: 350 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2620 !!! WARNING: HIR 108 has a net charge of 0.5140 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: 2.670534 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): -36.21300 12.09200 ymin,ymax (A): 31.29700 91.28500 zmin,zma (A): -24.51200 33.36500 x,y,z range (A): 48.30500 59.98801 57.87700 scale (grids/A): 2.670534 object centre (A): -12.06050 61.29100 4.426499 number of atom coordinates read : 2620 total number of charged atoms : 2481 net assigned charge : 2.014009 assigned positive charge : 410.5027 centred at (gu) : 91.75148 81.68894 80.42682 assigned negative charge : -408.4894 centred at (gu) : 92.28630 81.15748 79.81245 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 158104 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24792 grid for indexing accessible points = 1.400000 m= 72781 mr = 110324 m= 20798 mr = 56829 m= 3677 mr = 15196 m= 313 mr = 2400 m= 4 mr = 115 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8600000 number of dielectric boundary points 70813 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 19846 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) : 1.780356 object centre at (A) : -12.06050 61.29100 4.426499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.0990609E-02 6.8707220E-02 midg,1,midg; midg,igrid,midg -0.4420328 0.2914049 1,midg,midg; igrid,midg,midg 0.1417817 -0.1415412 gauss-seidel spectral radius is 0.9992085 estimated iterations to convergence 281 setup time was (sec) 1.130000 now iterating at: 13:12:58 rms-change max change #iterations 9.404235 305.2551 at 10iterations 5.434802 139.3947 at 20iterations 3.094924 70.40334 at 30iterations 1.763188 37.81552 at 40iterations 1.000232 23.75957 at 50iterations 0.5654438 11.57807 at 60iterations 0.3200769 7.132997 at 70iterations 0.1809403 3.787951 at 80iterations 0.1020686 2.094177 at 90iterations 5.7627618E-02 1.131760 at 100iterations 3.2556772E-02 0.6537628 at 110iterations 1.8374670E-02 0.3719492 at 120iterations 1.0361449E-02 0.2107968 at 130iterations 5.8395900E-03 0.1135712 at 140iterations 3.2971413E-03 7.5869560E-02 at 150iterations 1.8576136E-03 3.6443233E-02 at 160iterations 1.0512668E-03 2.1894932E-02 at 170iterations 5.9722678E-04 1.4001846E-02 at 180iterations finished qdiffx linear iterations at : 13:13:10 total time elapsed so far: 13.50000 # loops : 180 mean,max change (kT/e) : 5.9722678E-04 1.4001846E-02 energy calculations done at 13.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.64000 DelPhi exited at 13:13:11 13.637u 0.267s 0:14.52 95.6% 0+0k 0+0io 0pf+0w