Sat Oct 8 14:44:55 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 14:44:55 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3029 !!! WARNING: NDP 318 has a net charge of -3.0000 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: 0.6382330 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): -12.21600 43.56300 ymin,ymax (A): -22.92700 22.32900 zmin,zma (A): -6.598000 48.01000 x,y,z range (A): 55.77900 45.25600 54.60800 scale (grids/A): 0.6382330 object centre (A): 15.67350 -0.2989998 20.70600 number of atom coordinates read : 3029 total number of charged atoms : 2882 net assigned charge : -1.999993 assigned positive charge : 452.5276 centred at (gu) : 88.87154 89.84743 91.17116 assigned negative charge : -454.5283 centred at (gu) : 88.82748 89.74975 91.13576 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8270 nv = 96 ne = 84 npr = 63350 no. pairs analyzed = 63350 no. exposed pairs = 3467 no. arc points = 24487 no. surface atoms = 1175 nbur = 1854 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 439 mr = 4851 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3829 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2346 ## 204 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 9952 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.7143761E-09 2.4584788E-09 midg,1,midg; midg,igrid,midg -1.6061520E-08 9.5040837E-09 1,midg,midg; igrid,midg,midg -1.0809925E-08 2.2997704E-09 gauss-seidel spectral radius is 0.9873149 estimated iterations to convergence 73 setup time was (sec) 0.6800000 now iterating at: 14:44:56 rms-change max change #iterations 0.1543705 21.81636 at 10iterations 1.5374589E-02 2.088193 at 20iterations 1.5875952E-03 0.2141995 at 30iterations 1.6363952E-04 2.0431519E-02 at 40iterations 1.9659803E-05 2.6779175E-03 at 50iterations finished qdiffx linear iterations at : 14:45:00 total time elapsed so far: 4.630000 # loops : 50 mean,max change (kT/e) : 1.9659803E-05 2.6779175E-03 energy calculations done at 4.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.800000 DelPhi exited at 14:45:01 4.801u 0.401s 0:05.47 95.0% 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 Sat Oct 8 2011 at 14:45:01 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3029 !!! WARNING: NDP 318 has a net charge of -3.0000 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: 1.914699 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): -12.21600 43.56300 ymin,ymax (A): -22.92700 22.32900 zmin,zma (A): -6.598000 48.01000 x,y,z range (A): 55.77900 45.25600 54.60800 scale (grids/A): 1.914699 object centre (A): 15.67350 -0.2989998 20.70600 number of atom coordinates read : 3029 total number of charged atoms : 2882 net assigned charge : -1.999993 assigned positive charge : 452.5276 centred at (gu) : 86.61415 89.54165 93.51279 assigned negative charge : -454.5283 centred at (gu) : 86.48204 89.24887 93.40697 start vw surface at 0.1300000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 89931 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24487 grid for indexing accessible points = 1.400000 m= 32290 mr = 64893 m= 4706 mr = 24292 m= 274 mr = 2796 m= 3 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 215 time to turn everything in is 0.7200000 number of dielectric boundary points 35117 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 187 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 22727 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) : 0.6382330 object centre at (A) : 15.67350 -0.2989998 20.70600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1895762E-02 3.1210142E-03 midg,1,midg; midg,igrid,midg -7.8791957E-03 1.6566779E-02 1,midg,midg; igrid,midg,midg -3.9560597E-02 1.5371859E-02 gauss-seidel spectral radius is 0.9986858 estimated iterations to convergence 219 setup time was (sec) 1.040000 now iterating at: 14:45:02 rms-change max change #iterations 4.680963 179.9038 at 10iterations 2.236844 64.27658 at 20iterations 1.063001 32.55374 at 30iterations 0.5060516 15.04436 at 40iterations 0.2405464 6.894279 at 50iterations 0.1146806 3.548134 at 60iterations 5.4501332E-02 1.600010 at 70iterations 2.5909178E-02 0.7277412 at 80iterations 1.2368890E-02 0.3598766 at 90iterations 5.8737728E-03 0.1738796 at 100iterations 2.7987456E-03 9.0393066E-02 at 110iterations 1.3375306E-03 3.9272308E-02 at 120iterations finished qdiffx linear iterations at : 14:45:12 total time elapsed so far: 10.99000 # loops : 120 mean,max change (kT/e) : 1.3375306E-03 3.9272308E-02 energy calculations done at 10.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.16000 DelPhi exited at 14:45:13 11.160u 0.453s 0:11.89 97.6% 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 14:45:13 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3029 !!! WARNING: NDP 318 has a net charge of -3.0000 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: 2.872049 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): -12.21600 43.56300 ymin,ymax (A): -22.92700 22.32900 zmin,zma (A): -6.598000 48.01000 x,y,z range (A): 55.77900 45.25600 54.60800 scale (grids/A): 2.872049 object centre (A): 15.67350 -0.2989998 20.70600 number of atom coordinates read : 3029 total number of charged atoms : 2882 net assigned charge : -1.999993 assigned positive charge : 452.5276 centred at (gu) : 84.92113 89.31233 95.26895 assigned negative charge : -454.5283 centred at (gu) : 84.72301 88.87334 95.11051 start vw surface at 0.1400000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 207890 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24487 grid for indexing accessible points = 1.400000 m= 106635 mr = 156637 m= 37151 mr = 88957 m= 8289 mr = 29776 m= 1133 mr = 5988 m= 61 mr = 725 m= 0 mr = 39 time to grow re-entrant surface = 1.160000 no. cavity mid-points inaccessible to solvent = 737 time to turn everything in is 1.910000 number of dielectric boundary points 79037 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.040000 number of grid points assigned charge 23056 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) : 1.914699 object centre at (A) : 15.67350 -0.2989998 20.70600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3984577E-02 0.1629268 midg,1,midg; midg,igrid,midg -6.2745780E-02 0.1874847 1,midg,midg; igrid,midg,midg -0.5854986 0.2246773 gauss-seidel spectral radius is 0.9992764 estimated iterations to convergence 293 setup time was (sec) 2.240000 now iterating at: 14:45:15 rms-change max change #iterations 10.94628 426.0817 at 10iterations 6.428652 125.1040 at 20iterations 3.754069 75.68587 at 30iterations 2.188529 37.79240 at 40iterations 1.273289 22.36090 at 50iterations 0.7392105 15.01725 at 60iterations 0.4298726 6.733185 at 70iterations 0.2492360 4.427685 at 80iterations 0.1444905 2.519207 at 90iterations 8.3740257E-02 1.603237 at 100iterations 4.8388828E-02 0.8911629 at 110iterations 2.8038271E-02 0.4653285 at 120iterations 1.6220026E-02 0.2543062 at 130iterations 9.3847066E-03 0.1531620 at 140iterations 5.4221097E-03 8.5350037E-02 at 150iterations 3.1382835E-03 5.3977966E-02 at 160iterations 1.8181968E-03 3.5479546E-02 at 170iterations 1.0518990E-03 1.6555786E-02 at 180iterations finished qdiffx linear iterations at : 14:45:32 total time elapsed so far: 19.08000 # loops : 180 mean,max change (kT/e) : 1.0518990E-03 1.6555786E-02 energy calculations done at 19.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.25000 DelPhi exited at 14:45:33 19.252u 0.500s 0:20.15 98.0% 0+0k 0+0io 0pf+0w