Mon Oct 10 20:19:07 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 20:19:08 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2734 !!! WARNING: HIR 117 has a net charge of 0.5140 !!! WARNING: HIR 243 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6303898 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): -10.30000 45.52900 ymin,ymax (A): 32.11200 85.52500 zmin,zma (A): -10.95400 45.51900 x,y,z range (A): 55.82900 53.41300 56.47300 scale (grids/A): 0.6303898 object centre (A): 17.61450 58.81850 17.28250 number of atom coordinates read : 2734 total number of charged atoms : 2597 net assigned charge : 1.528019 assigned positive charge : 406.9706 centred at (gu) : 89.12864 88.90940 89.54927 assigned negative charge : -405.4438 centred at (gu) : 89.17012 88.90687 89.58624 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7365 nv = 96 ne = 84 npr = 54243 no. pairs analyzed = 54243 no. exposed pairs = 3846 no. arc points = 27542 no. surface atoms = 1266 nbur = 1468 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 412 mr = 3565 m= 4 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 4177 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2672 ## 213 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8792 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.5809011E-09 -1.6537384E-09 midg,1,midg; midg,igrid,midg 1.7437778E-09 1.4819275E-09 1,midg,midg; igrid,midg,midg 6.6264727E-09 -1.8515942E-09 gauss-seidel spectral radius is 0.9869909 estimated iterations to convergence 72 setup time was (sec) 0.5900000 now iterating at: 20:19:08 rms-change max change #iterations 0.1374994 18.71932 at 10iterations 1.3109453E-02 1.927963 at 20iterations 1.2707614E-03 0.1797371 at 30iterations 1.2894289E-04 1.9775391E-02 at 40iterations 1.7701946E-05 2.9678345E-03 at 50iterations finished qdiffx linear iterations at : 20:19:12 total time elapsed so far: 4.140000 # loops : 50 mean,max change (kT/e) : 1.7701946E-05 2.9678345E-03 energy calculations done at 4.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.320000 DelPhi exited at 20:19:12 4.328u 0.279s 0:04.89 93.8% 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 Mon Oct 10 2011 at 20:19:12 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2734 !!! WARNING: HIR 117 has a net charge of 0.5140 !!! WARNING: HIR 243 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.891169 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): -10.30000 45.52900 ymin,ymax (A): 32.11200 85.52500 zmin,zma (A): -10.95400 45.51900 x,y,z range (A): 55.82900 53.41300 56.47300 scale (grids/A): 1.891169 object centre (A): 17.61450 58.81850 17.28250 number of atom coordinates read : 2734 total number of charged atoms : 2597 net assigned charge : 1.528019 assigned positive charge : 406.9706 centred at (gu) : 87.38559 86.72753 88.64709 assigned negative charge : -405.4438 centred at (gu) : 87.51022 86.72057 88.75858 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 78186 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27542 grid for indexing accessible points = 1.400000 m= 27792 mr = 50594 m= 4655 mr = 19205 m= 251 mr = 2529 m= 4 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 38512 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 152 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 20404 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) : 0.6303898 object centre at (A) : 17.61450 58.81850 17.28250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9381674E-03 -2.7347002E-02 midg,1,midg; midg,igrid,midg 4.2844925E-02 2.6228927E-02 1,midg,midg; igrid,midg,midg 7.9735974E-03 -5.0916760E-03 gauss-seidel spectral radius is 0.9986497 estimated iterations to convergence 216 setup time was (sec) 0.9400000 now iterating at: 20:19:14 rms-change max change #iterations 4.285573 157.3626 at 10iterations 2.009672 66.90493 at 20iterations 0.9395095 32.97372 at 30iterations 0.4388239 14.05773 at 40iterations 0.2063932 6.685630 at 50iterations 9.6795000E-02 2.986441 at 60iterations 4.5315426E-02 1.568859 at 70iterations 2.1173228E-02 0.6837139 at 80iterations 9.9854246E-03 0.3170624 at 90iterations 4.6828152E-03 0.1623306 at 100iterations 2.2023630E-03 7.5360775E-02 at 110iterations 1.0355490E-03 3.3721924E-02 at 120iterations finished qdiffx linear iterations at : 20:19:23 total time elapsed so far: 9.840000 # loops : 120 mean,max change (kT/e) : 1.0355490E-03 3.3721924E-02 energy calculations done at 9.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.03000 DelPhi exited at 20:19:23 10.029u 0.344s 0:10.76 96.2% 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 Mon Oct 10 2011 at 20:19:23 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2734 !!! WARNING: HIR 117 has a net charge of 0.5140 !!! WARNING: HIR 243 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.836754 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): -10.30000 45.52900 ymin,ymax (A): 32.11200 85.52500 zmin,zma (A): -10.95400 45.51900 x,y,z range (A): 55.82900 53.41300 56.47300 scale (grids/A): 2.836754 object centre (A): 17.61450 58.81850 17.28250 number of atom coordinates read : 2734 total number of charged atoms : 2597 net assigned charge : 1.528019 assigned positive charge : 406.9706 centred at (gu) : 86.07812 85.09115 87.97062 assigned negative charge : -405.4438 centred at (gu) : 86.26536 85.08074 88.13791 start vw surface at 0.1500000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 180693 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27542 grid for indexing accessible points = 1.400000 m= 88144 mr = 123963 m= 33085 mr = 68938 m= 8055 mr = 25242 m= 1006 mr = 5456 m= 46 mr = 512 m= 0 mr = 12 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.560000 number of dielectric boundary points 86906 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 20772 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) : 1.891169 object centre at (A) : 17.61450 58.81850 17.28250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.1019313E-02 -0.2438935 midg,1,midg; midg,igrid,midg 0.6386634 0.3924814 1,midg,midg; igrid,midg,midg 0.2432329 -7.5240515E-02 gauss-seidel spectral radius is 0.9992810 estimated iterations to convergence 294 setup time was (sec) 1.910000 now iterating at: 20:19:25 rms-change max change #iterations 10.36913 345.4885 at 10iterations 6.190732 130.6067 at 20iterations 3.668473 79.42760 at 30iterations 2.167794 45.94367 at 40iterations 1.271600 26.86821 at 50iterations 0.7434071 16.48097 at 60iterations 0.4336604 8.294967 at 70iterations 0.2532008 4.974637 at 80iterations 0.1478396 2.821213 at 90iterations 8.5772544E-02 1.676689 at 100iterations 4.9952552E-02 0.9409543 at 110iterations 2.8995188E-02 0.5199888 at 120iterations 1.6858939E-02 0.3259201 at 130iterations 9.7756498E-03 0.1870575 at 140iterations 5.6776558E-03 0.1096468 at 150iterations 3.3019211E-03 6.5902710E-02 at 160iterations 1.9187320E-03 3.6064148E-02 at 170iterations 1.1216203E-03 2.0211220E-02 at 180iterations finished qdiffx linear iterations at : 20:19:40 total time elapsed so far: 16.29000 # loops : 180 mean,max change (kT/e) : 1.1216203E-03 2.0211220E-02 energy calculations done at 16.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.47000 DelPhi exited at 20:19:41 16.474u 0.305s 0:17.25 97.2% 0+0k 0+0io 0pf+0w