Mon Oct 10 13:55:13 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 Mon Oct 10 2011 at 13:55:13 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2569 !!! WARNING: GLM 46 has a net charge of -0.0940 !!! WARNING: GLM 118 has a net charge of -0.0940 !!! WARNING: GLU 264 has a net charge of -2.0000 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: 0.6383704 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): 13.14800 58.68900 ymin,ymax (A): 3.801000 53.44600 zmin,zma (A): -25.98800 29.77900 x,y,z range (A): 45.54100 49.64500 55.76700 scale (grids/A): 0.6383704 object centre (A): 35.91850 28.62350 1.895500 number of atom coordinates read : 2569 total number of charged atoms : 2422 net assigned charge : 1.312004 assigned positive charge : 381.2377 centred at (gu) : 91.46682 90.82387 89.26481 assigned negative charge : -379.9267 centred at (gu) : 91.41678 90.86253 89.46358 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6935 nv = 96 ne = 84 npr = 52146 no. pairs analyzed = 52146 no. exposed pairs = 3494 no. arc points = 24323 no. surface atoms = 1159 nbur = 1410 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 414 mr = 3581 m= 2 mr = 49 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 3721 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2362 ## 201 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8395 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6768156E-08 -1.7459136E-08 midg,1,midg; midg,igrid,midg 4.8666551E-09 -3.1577945E-09 1,midg,midg; igrid,midg,midg -2.7905511E-09 9.6767643E-09 gauss-seidel spectral radius is 0.9872893 estimated iterations to convergence 73 setup time was (sec) 0.3900000 now iterating at: 13:55:13 rms-change max change #iterations 0.1425892 24.94355 at 10iterations 1.4083087E-02 2.097967 at 20iterations 1.5886432E-03 0.2274046 at 30iterations 3.3347131E-04 4.9728394E-02 at 40iterations 1.1038733E-04 1.6435623E-02 at 50iterations finished qdiffx linear iterations at : 13:55:16 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 1.1038733E-04 1.6435623E-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) 3.410000 DelPhi exited at 13:55:17 3.417u 0.180s 0:03.94 91.1% 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 Mon Oct 10 2011 at 13:55:17 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2569 !!! WARNING: GLM 46 has a net charge of -0.0940 !!! WARNING: GLM 118 has a net charge of -0.0940 !!! WARNING: GLU 264 has a net charge of -2.0000 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: 1.915111 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): 13.14800 58.68900 ymin,ymax (A): 3.801000 53.44600 zmin,zma (A): -25.98800 29.77900 x,y,z range (A): 45.54100 49.64500 55.76700 scale (grids/A): 1.915111 object centre (A): 35.91850 28.62350 1.895500 number of atom coordinates read : 2569 total number of charged atoms : 2422 net assigned charge : 1.312004 assigned positive charge : 381.2377 centred at (gu) : 94.39994 92.47107 87.79366 assigned negative charge : -379.9267 centred at (gu) : 94.25001 92.58734 88.39058 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 74585 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24323 grid for indexing accessible points = 1.400000 m= 26946 mr = 49760 m= 4622 mr = 19211 m= 268 mr = 2804 m= 3 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 831 time to turn everything in is 0.3700000 number of dielectric boundary points 34580 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 152 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 19069 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) : 0.6383704 object centre at (A) : 35.91850 28.62350 1.895500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.5402364E-02 -4.2187250E-03 midg,1,midg; midg,igrid,midg 7.8530246E-03 -1.9723203E-03 1,midg,midg; igrid,midg,midg -6.2343511E-03 3.9574169E-03 gauss-seidel spectral radius is 0.9986547 estimated iterations to convergence 216 setup time was (sec) 0.5900000 now iterating at: 13:55:18 rms-change max change #iterations 4.300432 179.1065 at 10iterations 2.018613 62.60913 at 20iterations 0.9548189 41.74602 at 30iterations 0.4496934 14.87869 at 40iterations 0.2120294 7.401464 at 50iterations 9.9688053E-02 3.227898 at 60iterations 4.7128636E-02 1.568195 at 70iterations 2.2264224E-02 0.7027740 at 80iterations 1.0590200E-02 0.3284988 at 90iterations 5.0845556E-03 0.1761684 at 100iterations 2.4673133E-03 7.9818726E-02 at 110iterations 1.2388949E-03 4.3370247E-02 at 120iterations finished qdiffx linear iterations at : 13:55:25 total time elapsed so far: 7.780000 # loops : 120 mean,max change (kT/e) : 1.2388949E-03 4.3370247E-02 energy calculations done at 7.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.930000 DelPhi exited at 13:55:26 7.936u 0.199s 0:08.73 93.0% 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 Mon Oct 10 2011 at 13:55:26 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2569 !!! WARNING: GLM 46 has a net charge of -0.0940 !!! WARNING: GLM 118 has a net charge of -0.0940 !!! WARNING: GLU 264 has a net charge of -2.0000 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: 2.872667 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): 13.14800 58.68900 ymin,ymax (A): 3.801000 53.44600 zmin,zma (A): -25.98800 29.77900 x,y,z range (A): 45.54100 49.64500 55.76700 scale (grids/A): 2.872667 object centre (A): 35.91850 28.62350 1.895500 number of atom coordinates read : 2569 total number of charged atoms : 2422 net assigned charge : 1.312004 assigned positive charge : 381.2377 centred at (gu) : 96.59963 93.70643 86.69036 assigned negative charge : -379.9267 centred at (gu) : 96.37515 93.88101 87.58583 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 172430 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24323 grid for indexing accessible points = 1.400000 m= 85208 mr = 121404 m= 32280 mr = 67953 m= 8409 mr = 25337 m= 1188 mr = 6194 m= 64 mr = 741 m= 0 mr = 17 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 3041 time to turn everything in is 0.9700000 number of dielectric boundary points 77933 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 19374 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) : 1.915111 object centre at (A) : 35.91850 28.62350 1.895500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.114164 6.0406178E-02 midg,1,midg; midg,igrid,midg 0.1459592 8.8003632E-03 1,midg,midg; igrid,midg,midg -0.1581769 5.5515911E-02 gauss-seidel spectral radius is 0.9992648 estimated iterations to convergence 291 setup time was (sec) 1.220000 now iterating at: 13:55:27 rms-change max change #iterations 10.05346 336.0301 at 10iterations 5.879240 143.4221 at 20iterations 3.425177 68.59302 at 30iterations 1.990713 37.56331 at 40iterations 1.155565 21.55242 at 50iterations 0.6692270 12.26448 at 60iterations 0.3863394 6.829215 at 70iterations 0.2231706 4.108037 at 80iterations 0.1288508 2.406723 at 90iterations 7.4433379E-02 1.426872 at 100iterations 4.2842127E-02 0.8333435 at 110iterations 2.4701439E-02 0.4588997 at 120iterations 1.4246678E-02 0.2724915 at 130iterations 8.2209855E-03 0.1499481 at 140iterations 4.7618579E-03 0.1010933 at 150iterations 2.7580196E-03 5.4329872E-02 at 160iterations 1.6162568E-03 2.8205872E-02 at 170iterations 9.5974538E-04 1.7837524E-02 at 180iterations finished qdiffx linear iterations at : 13:55:39 total time elapsed so far: 13.26000 # loops : 180 mean,max change (kT/e) : 9.5974538E-04 1.7837524E-02 energy calculations done at 13.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.40000 DelPhi exited at 13:55:40 13.405u 0.200s 0:13.93 97.6% 0+0k 0+0io 0pf+0w