Tue Oct 11 04:22:56 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 Tue Oct 11 2011 at 04:22:56 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2779 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6459925 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): -14.92200 33.36800 ymin,ymax (A): 6.946000 55.34400 zmin,zma (A): 25.54000 80.64900 x,y,z range (A): 48.29000 48.39800 55.10900 scale (grids/A): 0.6459925 object centre (A): 9.223000 31.14500 53.09450 number of atom coordinates read : 2779 total number of charged atoms : 2626 net assigned charge : 2.162016 assigned positive charge : 419.0276 centred at (gu) : 90.19669 90.48437 88.17160 assigned negative charge : -416.8663 centred at (gu) : 90.51887 90.31127 88.15665 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7630 nv = 96 ne = 84 npr = 57336 no. pairs analyzed = 57336 no. exposed pairs = 3351 no. arc points = 23386 no. surface atoms = 1122 nbur = 1657 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 437 mr = 4327 m= 1 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.3100000 number of dielectric boundary points 3669 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2304 ## 233 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 9290 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3297753E-09 4.1311186E-09 midg,1,midg; midg,igrid,midg -1.9830432E-08 3.1931492E-08 1,midg,midg; igrid,midg,midg 4.7453980E-08 -4.7101377E-08 gauss-seidel spectral radius is 0.9875945 estimated iterations to convergence 73 setup time was (sec) 0.5600000 now iterating at: 04:22:57 rms-change max change #iterations 0.1584966 21.51277 at 10iterations 1.6273273E-02 2.399355 at 20iterations 1.6813253E-03 0.2269135 at 30iterations 1.9167327E-04 2.4726868E-02 at 40iterations 3.0768402E-05 4.4097900E-03 at 50iterations finished qdiffx linear iterations at : 04:22:59 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 3.0768402E-05 4.4097900E-03 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 04:23:00 3.362u 0.186s 0:03.88 91.2% 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 Tue Oct 11 2011 at 04:23:00 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2779 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 1.937977 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): -14.92200 33.36800 ymin,ymax (A): 6.946000 55.34400 zmin,zma (A): 25.54000 80.64900 x,y,z range (A): 48.29000 48.39800 55.10900 scale (grids/A): 1.937977 object centre (A): 9.223000 31.14500 53.09450 number of atom coordinates read : 2779 total number of charged atoms : 2626 net assigned charge : 2.162016 assigned positive charge : 419.0276 centred at (gu) : 90.58939 91.45277 84.51397 assigned negative charge : -416.8663 centred at (gu) : 91.55632 90.93356 84.46968 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 83020 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23386 grid for indexing accessible points = 1.400000 m= 30417 mr = 58748 m= 4852 mr = 22699 m= 286 mr = 3058 m= 2 mr = 105 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 3684 time to turn everything in is 0.5700000 number of dielectric boundary points 33967 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 124 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 20681 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) : 0.6459925 object centre at (A) : 9.223000 31.14500 53.09450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.6412990E-03 -2.0696219E-02 midg,1,midg; midg,igrid,midg -1.4299071E-02 3.4862697E-02 1,midg,midg; igrid,midg,midg 6.4974159E-02 -2.3010757E-02 gauss-seidel spectral radius is 0.9986949 estimated iterations to convergence 219 setup time was (sec) 0.8600000 now iterating at: 04:23:01 rms-change max change #iterations 4.570560 169.7902 at 10iterations 2.184375 73.35889 at 20iterations 1.039575 36.86421 at 30iterations 0.4965191 16.29627 at 40iterations 0.2373363 7.511813 at 50iterations 0.1132162 3.360804 at 60iterations 5.4057743E-02 1.568716 at 70iterations 2.5732219E-02 0.8468323 at 80iterations 1.2340126E-02 0.3540993 at 90iterations 5.8954926E-03 0.1680145 at 100iterations 2.8212480E-03 8.2054138E-02 at 110iterations 1.3452867E-03 4.0895462E-02 at 120iterations finished qdiffx linear iterations at : 04:23:08 total time elapsed so far: 7.410000 # loops : 120 mean,max change (kT/e) : 1.3452867E-03 4.0895462E-02 energy calculations done at 7.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.580000 DelPhi exited at 04:23:08 7.582u 0.256s 0:08.17 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 Tue Oct 11 2011 at 04:23:08 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2779 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 2.906966 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): -14.92200 33.36800 ymin,ymax (A): 6.946000 55.34400 zmin,zma (A): 25.54000 80.64900 x,y,z range (A): 48.29000 48.39800 55.10900 scale (grids/A): 2.906966 object centre (A): 9.223000 31.14500 53.09450 number of atom coordinates read : 2779 total number of charged atoms : 2626 net assigned charge : 2.162016 assigned positive charge : 419.0276 centred at (gu) : 90.88399 92.17916 81.77079 assigned negative charge : -416.8663 centred at (gu) : 92.33451 91.40020 81.70450 start vw surface at 0.1400000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 192503 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23386 grid for indexing accessible points = 1.400000 m= 98377 mr = 142573 m= 35398 mr = 81076 m= 8794 mr = 28683 m= 1343 mr = 6604 m= 92 mr = 930 m= 1 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 11962 time to turn everything in is 1.460000 number of dielectric boundary points 76599 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.600000 number of grid points assigned charge 21001 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) : 1.937977 object centre at (A) : 9.223000 31.14500 53.09450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1266835 -0.3574831 midg,1,midg; midg,igrid,midg -0.1711693 0.4194042 1,midg,midg; igrid,midg,midg 0.5636169 -0.1195741 gauss-seidel spectral radius is 0.9992703 estimated iterations to convergence 292 setup time was (sec) 1.760000 now iterating at: 04:23:10 rms-change max change #iterations 10.57243 417.3715 at 10iterations 6.194942 138.1574 at 20iterations 3.615158 74.91662 at 30iterations 2.109634 42.72163 at 40iterations 1.227606 22.33792 at 50iterations 0.7141119 13.04088 at 60iterations 0.4154157 7.752572 at 70iterations 0.2402349 4.646168 at 80iterations 0.1389555 2.424067 at 90iterations 8.0692865E-02 1.390785 at 100iterations 4.6628773E-02 0.8372359 at 110iterations 2.7046209E-02 0.4566040 at 120iterations 1.5683796E-02 0.2677879 at 130iterations 9.1040926E-03 0.1687241 at 140iterations 5.3019612E-03 9.2929840E-02 at 150iterations 3.1083431E-03 5.4495811E-02 at 160iterations 1.8409730E-03 3.5232544E-02 at 170iterations 1.1122350E-03 2.0347595E-02 at 180iterations finished qdiffx linear iterations at : 04:23:21 total time elapsed so far: 12.15000 # loops : 180 mean,max change (kT/e) : 1.1122350E-03 2.0347595E-02 energy calculations done at 12.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.33000 DelPhi exited at 04:23:21 12.335u 0.239s 0:12.97 96.8% 0+0k 0+0io 0pf+0w