Tue Oct 11 06:33:02 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 Tue Oct 11 2011 at 06:33:03 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2089 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 0.7183647 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): -40.95000 -0.6990000 ymin,ymax (A): -27.14600 18.75800 zmin,zma (A): -14.89600 34.66100 x,y,z range (A): 40.25100 45.90400 49.55700 scale (grids/A): 0.7183647 object centre (A): -20.82450 -4.194000 9.882500 number of atom coordinates read : 2089 total number of charged atoms : 1955 net assigned charge : 5.945010 assigned positive charge : 320.3760 centred at (gu) : 91.19166 89.85152 88.97414 assigned negative charge : -314.4311 centred at (gu) : 91.24802 89.99540 88.92741 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7300 nv = 96 ne = 84 npr = 41788 no. pairs analyzed = 41788 no. exposed pairs = 2554 no. arc points = 17385 no. surface atoms = 869 nbur = 1220 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 498 mr = 4189 m= 5 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3522 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1604 ## 172 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7997 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.2701966E-08 7.8108535E-08 midg,1,midg; midg,igrid,midg 1.5944184E-07 -2.6038700E-08 1,midg,midg; igrid,midg,midg 8.0507505E-08 3.6180392E-08 gauss-seidel spectral radius is 0.9898958 estimated iterations to convergence 81 setup time was (sec) 0.5300000 now iterating at: 06:33:03 rms-change max change #iterations 0.2190986 29.50496 at 10iterations 2.8178878E-02 4.166947 at 20iterations 3.9227712E-03 0.5151062 at 30iterations 6.3965766E-04 8.2311630E-02 at 40iterations 1.4950616E-04 1.9023895E-02 at 50iterations finished qdiffx linear iterations at : 06:33:06 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 1.4950616E-04 1.9023895E-02 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 06:33:07 3.486u 0.161s 0:04.08 89.2% 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 06:33:07 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2089 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 2.155094 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): -40.95000 -0.6990000 ymin,ymax (A): -27.14600 18.75800 zmin,zma (A): -14.89600 34.66100 x,y,z range (A): 40.25100 45.90400 49.55700 scale (grids/A): 2.155094 object centre (A): -20.82450 -4.194000 9.882500 number of atom coordinates read : 2089 total number of charged atoms : 1955 net assigned charge : 5.945010 assigned positive charge : 320.3760 centred at (gu) : 93.57487 89.55486 86.92233 assigned negative charge : -314.4311 centred at (gu) : 93.74414 89.98629 86.78233 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 77578 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17385 grid for indexing accessible points = 1.400000 m= 31254 mr = 55296 m= 6158 mr = 23702 m= 593 mr = 4061 m= 16 mr = 307 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 32233 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 94 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 15531 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) : 0.7183647 object centre at (A) : -20.82450 -4.194000 9.882500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0711362E-02 3.5370786E-02 midg,1,midg; midg,igrid,midg 4.8051734E-02 1.0630622E-02 1,midg,midg; igrid,midg,midg 2.1845318E-02 3.1377193E-02 gauss-seidel spectral radius is 0.9988614 estimated iterations to convergence 235 setup time was (sec) 0.9400000 now iterating at: 06:33:08 rms-change max change #iterations 4.825206 200.3133 at 10iterations 2.414455 73.25633 at 20iterations 1.214638 39.55729 at 30iterations 0.6080111 18.26540 at 40iterations 0.3050901 8.911852 at 50iterations 0.1531872 4.573818 at 60iterations 7.6512583E-02 2.219399 at 70iterations 3.8505103E-02 1.112788 at 80iterations 1.9464821E-02 0.6135750 at 90iterations 9.8126745E-03 0.3027897 at 100iterations 4.9954802E-03 0.1691055 at 110iterations 2.5633187E-03 7.7404976E-02 at 120iterations finished qdiffx linear iterations at : 06:33:15 total time elapsed so far: 7.770000 # loops : 120 mean,max change (kT/e) : 2.5633187E-03 7.7404976E-02 energy calculations done at 7.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.960000 DelPhi exited at 06:33:15 7.964u 0.211s 0:08.52 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 06:33:15 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2089 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 3.232641 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): -40.95000 -0.6990000 ymin,ymax (A): -27.14600 18.75800 zmin,zma (A): -14.89600 34.66100 x,y,z range (A): 40.25100 45.90400 49.55700 scale (grids/A): 3.232641 object centre (A): -20.82450 -4.194000 9.882500 number of atom coordinates read : 2089 total number of charged atoms : 1955 net assigned charge : 5.945010 assigned positive charge : 320.3760 centred at (gu) : 95.36223 89.33216 85.38356 assigned negative charge : -314.4311 centred at (gu) : 95.61617 89.97939 85.17360 start vw surface at 0.1600000 fill in re-entrant regions at 0.8700000 boundary points on vw surface= 178486 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17385 grid for indexing accessible points = 1.400000 m= 97345 mr = 132741 m= 39782 mr = 81228 m= 11686 mr = 32547 m= 2389 mr = 9048 m= 301 mr = 1662 m= 8 mr = 196 m= 0 mr = 3 time to grow re-entrant surface = 0.9599999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.950000 number of dielectric boundary points 72572 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.080000 number of grid points assigned charge 15640 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) : 2.155094 object centre at (A) : -20.82450 -4.194000 9.882500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3328194 0.1306796 midg,1,midg; midg,igrid,midg 0.3703283 0.1526430 1,midg,midg; igrid,midg,midg 0.1733560 0.3253382 gauss-seidel spectral radius is 0.9993055 estimated iterations to convergence 299 setup time was (sec) 2.250000 now iterating at: 06:33:18 rms-change max change #iterations 10.63391 317.7497 at 10iterations 6.310912 195.2611 at 20iterations 3.734519 72.66936 at 30iterations 2.205953 38.93264 at 40iterations 1.304195 24.36375 at 50iterations 0.7655026 14.32549 at 60iterations 0.4512196 7.525775 at 70iterations 0.2652607 4.736374 at 80iterations 0.1564531 2.815704 at 90iterations 9.1875777E-02 1.544047 at 100iterations 5.4181345E-02 0.9126606 at 110iterations 3.2075297E-02 0.5430369 at 120iterations 1.9141549E-02 0.3133841 at 130iterations 1.1590065E-02 0.2158947 at 140iterations 7.1966127E-03 0.1245651 at 150iterations 4.6269200E-03 8.7799072E-02 at 160iterations 3.1323379E-03 6.2980652E-02 at 170iterations 2.2404843E-03 4.0645599E-02 at 180iterations finished qdiffx linear iterations at : 06:33:28 total time elapsed so far: 12.83000 # loops : 180 mean,max change (kT/e) : 2.2404843E-03 4.0645599E-02 energy calculations done at 12.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.01000 DelPhi exited at 06:33:29 13.014u 0.270s 0:13.62 97.5% 0+0k 0+0io 0pf+0w