Tue Oct 11 08:33:28 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 08:33:28 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2750 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.6411642 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): -13.11900 36.89200 ymin,ymax (A): -26.82400 21.65100 zmin,zma (A): -10.21400 45.31000 x,y,z range (A): 50.01100 48.47500 55.52400 scale (grids/A): 0.6411642 object centre (A): 11.88650 -2.586500 17.54800 number of atom coordinates read : 2750 total number of charged atoms : 2592 net assigned charge : 1.926020 assigned positive charge : 418.6687 centred at (gu) : 90.53931 90.41393 91.79993 assigned negative charge : -416.7432 centred at (gu) : 90.31926 90.27446 91.75545 start vw surface at 0.1800000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7470 nv = 96 ne = 84 npr = 55717 no. pairs analyzed = 55717 no. exposed pairs = 3338 no. arc points = 23304 no. surface atoms = 1124 nbur = 1626 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 402 mr = 4210 m= 2 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3610 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2261 ## 232 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 9049 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.1253643E-09 1.2206942E-08 midg,1,midg; midg,igrid,midg -1.4319400E-08 2.2172117E-08 1,midg,midg; igrid,midg,midg -2.3534106E-08 3.4016470E-08 gauss-seidel spectral radius is 0.9874075 estimated iterations to convergence 73 setup time was (sec) 0.5300000 now iterating at: 08:33:28 rms-change max change #iterations 0.1557701 20.40109 at 10iterations 1.5805027E-02 2.358173 at 20iterations 1.6421820E-03 0.2247238 at 30iterations 1.9779149E-04 2.4755478E-02 at 40iterations 3.4768102E-05 4.1179657E-03 at 50iterations finished qdiffx linear iterations at : 08:33:31 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 3.4768102E-05 4.1179657E-03 energy calculations done at 3.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 08:33:32 3.315u 0.186s 0:03.88 89.9% 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 08:33:32 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2750 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.923492 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): -13.11900 36.89200 ymin,ymax (A): -26.82400 21.65100 zmin,zma (A): -10.21400 45.31000 x,y,z range (A): 50.01100 48.47500 55.52400 scale (grids/A): 1.923492 object centre (A): 11.88650 -2.586500 17.54800 number of atom coordinates read : 2750 total number of charged atoms : 2592 net assigned charge : 1.926020 assigned positive charge : 418.6687 centred at (gu) : 91.61743 91.24134 95.39941 assigned negative charge : -416.7432 centred at (gu) : 90.95744 90.82294 95.26599 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 81138 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23304 grid for indexing accessible points = 1.400000 m= 29771 mr = 57242 m= 4864 mr = 22180 m= 334 mr = 3164 m= 7 mr = 140 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 920 time to turn everything in is 0.5700000 number of dielectric boundary points 33388 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 178 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 20443 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) : 0.6411642 object centre at (A) : 11.88650 -2.586500 17.54800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0660850E-02 1.5788451E-03 midg,1,midg; midg,igrid,midg -1.7968776E-02 7.1555530E-03 1,midg,midg; igrid,midg,midg -1.2991604E-02 6.6331431E-02 gauss-seidel spectral radius is 0.9986765 estimated iterations to convergence 218 setup time was (sec) 0.8200000 now iterating at: 08:33:33 rms-change max change #iterations 4.536468 190.3545 at 10iterations 2.148035 70.86546 at 20iterations 1.019273 30.17438 at 30iterations 0.4849423 17.53242 at 40iterations 0.2299791 7.624973 at 50iterations 0.1096720 3.345295 at 60iterations 5.1933024E-02 1.590957 at 70iterations 2.4658436E-02 0.7445679 at 80iterations 1.1739960E-02 0.3748856 at 90iterations 5.5830949E-03 0.1755428 at 100iterations 2.6598591E-03 8.1027985E-02 at 110iterations 1.2744097E-03 3.9753914E-02 at 120iterations finished qdiffx linear iterations at : 08:33:39 total time elapsed so far: 6.860000 # loops : 120 mean,max change (kT/e) : 1.2744097E-03 3.9753914E-02 energy calculations done at 6.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.040000 DelPhi exited at 08:33:39 7.040u 0.184s 0:07.52 96.0% 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 Tue Oct 11 2011 at 08:33:39 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2750 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 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: 2.885239 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): -13.11900 36.89200 ymin,ymax (A): -26.82400 21.65100 zmin,zma (A): -10.21400 45.31000 x,y,z range (A): 50.01100 48.47500 55.52400 scale (grids/A): 2.885239 object centre (A): 11.88650 -2.586500 17.54800 number of atom coordinates read : 2750 total number of charged atoms : 2592 net assigned charge : 1.926020 assigned positive charge : 418.6687 centred at (gu) : 92.42600 91.86182 98.09892 assigned negative charge : -416.7432 centred at (gu) : 91.43614 91.23439 97.89896 start vw surface at 0.1500000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 187733 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23304 grid for indexing accessible points = 1.400000 m= 96119 mr = 138277 m= 35324 mr = 79407 m= 8818 mr = 28702 m= 1360 mr = 6723 m= 110 mr = 959 m= 3 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.8200000 no. cavity mid-points inaccessible to solvent = 3253 time to turn everything in is 1.400000 number of dielectric boundary points 75343 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.530000 number of grid points assigned charge 20735 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) : 1.923492 object centre at (A) : 11.88650 -2.586500 17.54800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3127042 0.1250019 midg,1,midg; midg,igrid,midg -0.1801999 1.1552275E-02 1,midg,midg; igrid,midg,midg -0.1033957 0.5826324 gauss-seidel spectral radius is 0.9992679 estimated iterations to convergence 292 setup time was (sec) 1.680000 now iterating at: 08:33:41 rms-change max change #iterations 10.47752 397.0282 at 10iterations 6.128901 135.3432 at 20iterations 3.578573 67.08607 at 30iterations 2.082947 43.18773 at 40iterations 1.207044 21.46050 at 50iterations 0.6994356 13.46883 at 60iterations 0.4061040 7.419768 at 70iterations 0.2351105 4.449605 at 80iterations 0.1362088 2.290235 at 90iterations 7.8721322E-02 1.427063 at 100iterations 4.5459375E-02 0.8195268 at 110iterations 2.6391540E-02 0.4617157 at 120iterations 1.5260847E-02 0.2819042 at 130iterations 8.8536851E-03 0.2083282 at 140iterations 5.1349094E-03 9.9456787E-02 at 150iterations 2.9977609E-03 5.3747177E-02 at 160iterations 1.7591757E-03 3.0536652E-02 at 170iterations 1.0439034E-03 1.9012451E-02 at 180iterations finished qdiffx linear iterations at : 08:33:52 total time elapsed so far: 12.19000 # loops : 180 mean,max change (kT/e) : 1.0439034E-03 1.9012451E-02 energy calculations done at 12.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.36000 DelPhi exited at 08:33:52 12.364u 0.217s 0:13.06 96.2% 0+0k 0+0io 0pf+0w