Sun Oct 9 20:42:16 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 Sun Oct 9 2011 at 20:42:16 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4959 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5627213 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): 3.385000 64.47800 ymin,ymax (A): -7.836000 53.63800 zmin,zma (A): -1.144000 62.12000 x,y,z range (A): 61.09300 61.47400 63.26400 scale (grids/A): 0.5627213 object centre (A): 33.93150 22.90100 30.48800 number of atom coordinates read : 4959 total number of charged atoms : 4803 net assigned charge : 1.635043 assigned positive charge : 763.4233 centred at (gu) : 88.15865 89.05252 89.05734 assigned negative charge : -761.7936 centred at (gu) : 88.04675 89.05576 89.03551 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 10215 nv = 96 ne = 84 npr = 101596 no. pairs analyzed = 101596 no. exposed pairs = 5719 no. arc points = 38373 no. surface atoms = 1952 nbur = 3007 mkacc time = 0.2100000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 475 mr = 5914 m= 2 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 4743 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3933 ## 409 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 13379 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.6809202E-10 5.5529203E-10 midg,1,midg; midg,igrid,midg 3.9061424E-10 1.4230836E-10 1,midg,midg; igrid,midg,midg -3.3406102E-09 1.6266748E-09 gauss-seidel spectral radius is 0.9838522 estimated iterations to convergence 65 setup time was (sec) 0.6800000 now iterating at: 20:42:17 rms-change max change #iterations 0.1192903 17.45274 at 10iterations 1.1763986E-02 1.532898 at 20iterations 3.7028661E-03 0.4490166 at 30iterations 1.7329513E-03 0.2059851 at 40iterations 8.2948443E-04 0.1024208 at 50iterations finished qdiffx linear iterations at : 20:42:20 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 8.2948443E-04 0.1024208 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.600000 DelPhi exited at 20:42:21 3.607u 0.239s 0:04.15 92.2% 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 Sun Oct 9 2011 at 20:42:21 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4959 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.688164 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): 3.385000 64.47800 ymin,ymax (A): -7.836000 53.63800 zmin,zma (A): -1.144000 62.12000 x,y,z range (A): 61.09300 61.47400 63.26400 scale (grids/A): 1.688164 object centre (A): 33.93150 22.90100 30.48800 number of atom coordinates read : 4959 total number of charged atoms : 4803 net assigned charge : 1.635043 assigned positive charge : 763.4233 centred at (gu) : 84.47441 87.15598 87.17079 assigned negative charge : -761.7936 centred at (gu) : 84.14001 87.16734 87.10646 start vw surface at 0.2000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 113573 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38373 grid for indexing accessible points = 1.400000 m= 40764 mr = 82895 m= 5209 mr = 29922 m= 218 mr = 2965 m= 0 mr = 47 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 185 time to turn everything in is 0.7700000 number of dielectric boundary points 43935 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 350 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 37053 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) : 0.5627213 object centre at (A) : 33.93150 22.90100 30.48800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0289380E-02 -2.9442979E-02 midg,1,midg; midg,igrid,midg 2.3146357E-02 1.5338923E-02 1,midg,midg; igrid,midg,midg -2.8289353E-02 4.2027254E-02 gauss-seidel spectral radius is 0.9984823 estimated iterations to convergence 204 setup time was (sec) 1.080000 now iterating at: 20:42:22 rms-change max change #iterations 4.961564 172.8446 at 10iterations 2.222569 72.71895 at 20iterations 1.003905 26.36792 at 30iterations 0.4517524 11.81862 at 40iterations 0.2039872 5.705669 at 50iterations 9.2430241E-02 2.535124 at 60iterations 4.2022504E-02 1.183555 at 70iterations 1.9473482E-02 0.5449136 at 80iterations 9.4948830E-03 0.2676849 at 90iterations 5.0536883E-03 0.1540527 at 100iterations 3.0516449E-03 8.8266373E-02 at 110iterations 2.0805299E-03 6.1111450E-02 at 120iterations finished qdiffx linear iterations at : 20:42:29 total time elapsed so far: 8.320000 # loops : 120 mean,max change (kT/e) : 2.0805299E-03 6.1111450E-02 energy calculations done at 8.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.510000 DelPhi exited at 20:42:30 8.516u 0.248s 0:09.15 95.6% 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 Sun Oct 9 2011 at 20:42:30 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4959 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.532246 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): 3.385000 64.47800 ymin,ymax (A): -7.836000 53.63800 zmin,zma (A): -1.144000 62.12000 x,y,z range (A): 61.09300 61.47400 63.26400 scale (grids/A): 2.532246 object centre (A): 33.93150 22.90100 30.48800 number of atom coordinates read : 4959 total number of charged atoms : 4803 net assigned charge : 1.635043 assigned positive charge : 763.4233 centred at (gu) : 81.71140 85.73370 85.75586 assigned negative charge : -761.7936 centred at (gu) : 81.21015 85.75090 85.65972 start vw surface at 0.1900000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 263555 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38373 grid for indexing accessible points = 1.400000 m= 136004 mr = 200692 m= 44960 mr = 112196 m= 8828 mr = 35400 m= 844 mr = 6270 m= 16 mr = 456 m= 0 mr = 5 time to grow re-entrant surface = 1.190000 no. cavity mid-points inaccessible to solvent = 632 time to turn everything in is 1.940000 number of dielectric boundary points 99188 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 2.100000 number of grid points assigned charge 38400 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) : 1.688164 object centre at (A) : 33.93150 22.90100 30.48800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5383429 -0.7337279 midg,1,midg; midg,igrid,midg 5.0294925E-02 9.3818426E-02 1,midg,midg; igrid,midg,midg -0.5255750 0.7591627 gauss-seidel spectral radius is 0.9992636 estimated iterations to convergence 291 setup time was (sec) 2.280000 now iterating at: 20:42:32 rms-change max change #iterations 12.41611 310.8292 at 10iterations 7.350324 156.0554 at 20iterations 4.315639 73.98869 at 30iterations 2.527843 44.43205 at 40iterations 1.478784 31.61620 at 50iterations 0.8605676 14.09605 at 60iterations 0.4992547 7.909805 at 70iterations 0.2896956 4.646361 at 80iterations 0.1679822 2.510026 at 90iterations 9.7477436E-02 1.649429 at 100iterations 5.6435231E-02 0.9836636 at 110iterations 3.2844078E-02 0.5309362 at 120iterations 1.9301107E-02 0.2945499 at 130iterations 1.1540194E-02 0.1881251 at 140iterations 7.1173706E-03 0.1150570 at 150iterations 4.6099443E-03 9.0405464E-02 at 160iterations 3.2078519E-03 5.7505608E-02 at 170iterations 2.3932057E-03 4.1268528E-02 at 180iterations finished qdiffx linear iterations at : 20:42:45 total time elapsed so far: 14.56000 # loops : 180 mean,max change (kT/e) : 2.3932057E-03 4.1268528E-02 energy calculations done at 14.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.75000 DelPhi exited at 20:42:45 14.748u 0.266s 0:15.31 97.9% 0+0k 0+0io 0pf+0w