Sat Oct 8 18:52:51 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 18:52:51 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2592 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 0.6246929 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): -31.38200 17.48400 ymin,ymax (A): -23.65400 23.07100 zmin,zma (A): -12.69600 44.29200 x,y,z range (A): 48.86600 46.72500 56.98800 scale (grids/A): 0.6246929 object centre (A): -6.949000 -0.2915001 15.79800 number of atom coordinates read : 2592 total number of charged atoms : 2462 net assigned charge : 4.500007 assigned positive charge : 393.3700 centred at (gu) : 88.44167 89.26210 89.95893 assigned negative charge : -388.8705 centred at (gu) : 88.33092 89.30281 89.85501 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6672 nv = 96 ne = 84 npr = 53653 no. pairs analyzed = 53653 no. exposed pairs = 3018 no. arc points = 21355 no. surface atoms = 1014 nbur = 1578 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 325 mr = 3784 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 124 time to turn everything in is 0.3500000 number of dielectric boundary points 3178 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2138 ## 229 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8151 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.7255661E-09 1.1997963E-08 midg,1,midg; midg,igrid,midg 8.6634495E-09 1.0428832E-09 1,midg,midg; igrid,midg,midg -6.1082410E-09 8.9937080E-09 gauss-seidel spectral radius is 0.9867244 estimated iterations to convergence 71 setup time was (sec) 0.6200000 now iterating at: 18:52:52 rms-change max change #iterations 0.1341988 20.21638 at 10iterations 1.2587046E-02 2.466652 at 20iterations 1.1750758E-03 0.1886005 at 30iterations 1.0850465E-04 1.6911507E-02 at 40iterations 1.0324348E-05 1.4429092E-03 at 50iterations finished qdiffx linear iterations at : 18:52:55 total time elapsed so far: 3.890000 # loops : 50 mean,max change (kT/e) : 1.0324348E-05 1.4429092E-03 energy calculations done at 3.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.060000 DelPhi exited at 18:52:55 4.065u 0.264s 0:04.58 94.3% 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 18:52:55 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2592 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 1.874079 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): -31.38200 17.48400 ymin,ymax (A): -23.65400 23.07100 zmin,zma (A): -12.69600 44.29200 x,y,z range (A): 48.86600 46.72500 56.98800 scale (grids/A): 1.874079 object centre (A): -6.949000 -0.2915001 15.79800 number of atom coordinates read : 2592 total number of charged atoms : 2462 net assigned charge : 4.500007 assigned positive charge : 393.3700 centred at (gu) : 85.32455 87.78596 89.87637 assigned negative charge : -388.8705 centred at (gu) : 84.99260 87.90812 89.56464 start vw surface at 0.1400000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 72634 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21355 grid for indexing accessible points = 1.400000 m= 25827 mr = 51178 m= 3877 mr = 19450 m= 249 mr = 2534 m= 4 mr = 87 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 5828 time to turn everything in is 0.6300000 number of dielectric boundary points 29343 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 181 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 19315 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) : 0.6246929 object centre at (A) : -6.949000 -0.2915001 15.79800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4097107E-02 3.0682597E-02 midg,1,midg; midg,igrid,midg 1.1985477E-02 4.1299997E-04 1,midg,midg; igrid,midg,midg -2.5908524E-04 3.4491107E-02 gauss-seidel spectral radius is 0.9985884 estimated iterations to convergence 211 setup time was (sec) 0.9100000 now iterating at: 18:52:56 rms-change max change #iterations 4.104708 164.9653 at 10iterations 1.892870 63.95813 at 20iterations 0.8769934 28.33375 at 30iterations 0.4042729 13.54195 at 40iterations 0.1874589 6.082411 at 50iterations 8.6731389E-02 3.256374 at 60iterations 4.0062722E-02 1.441620 at 70iterations 1.8542474E-02 0.5661268 at 80iterations 8.6030904E-03 0.2697372 at 90iterations 3.9731092E-03 0.1278648 at 100iterations 1.8435322E-03 5.8925629E-02 at 110iterations 8.5386122E-04 2.9380798E-02 at 120iterations finished qdiffx linear iterations at : 18:53:05 total time elapsed so far: 9.140000 # loops : 120 mean,max change (kT/e) : 8.5386122E-04 2.9380798E-02 energy calculations done at 9.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.320000 DelPhi exited at 18:53:05 9.319u 0.324s 0:09.91 97.1% 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 Sat Oct 8 2011 at 18:53:05 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2592 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 2.811118 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): -31.38200 17.48400 ymin,ymax (A): -23.65400 23.07100 zmin,zma (A): -12.69600 44.29200 x,y,z range (A): 48.86600 46.72500 56.98800 scale (grids/A): 2.811118 object centre (A): -6.949000 -0.2915001 15.79800 number of atom coordinates read : 2592 total number of charged atoms : 2462 net assigned charge : 4.500007 assigned positive charge : 393.3700 centred at (gu) : 82.98691 86.67883 89.81434 assigned negative charge : -388.8705 centred at (gu) : 82.48883 86.86204 89.34693 start vw surface at 0.1600000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 167878 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21355 grid for indexing accessible points = 1.400000 m= 84942 mr = 123455 m= 29754 mr = 70475 m= 7060 mr = 24336 m= 1128 mr = 5500 m= 57 mr = 835 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 19070 time to turn everything in is 1.610000 number of dielectric boundary points 66201 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.750000 number of grid points assigned charge 19689 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) : 1.874079 object centre at (A) : -6.949000 -0.2915001 15.79800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.5773524E-02 0.3972539 midg,1,midg; midg,igrid,midg 0.1539826 -7.6080165E-03 1,midg,midg; igrid,midg,midg 7.1593043E-03 0.4255532 gauss-seidel spectral radius is 0.9992399 estimated iterations to convergence 286 setup time was (sec) 1.930000 now iterating at: 18:53:07 rms-change max change #iterations 9.577713 344.7887 at 10iterations 5.498984 155.0992 at 20iterations 3.139157 74.33751 at 30iterations 1.791837 32.38379 at 40iterations 1.023356 19.78070 at 50iterations 0.5828936 11.01696 at 60iterations 0.3321839 6.423977 at 70iterations 0.1892022 3.697244 at 80iterations 0.1078051 2.138780 at 90iterations 6.1389491E-02 1.105489 at 100iterations 3.4913223E-02 0.6854057 at 110iterations 1.9882204E-02 0.3413544 at 120iterations 1.1334425E-02 0.2203960 at 130iterations 6.4655668E-03 0.1185603 at 140iterations 3.6696473E-03 6.6444397E-02 at 150iterations 2.0901232E-03 4.7954559E-02 at 160iterations 1.1949948E-03 2.1991730E-02 at 170iterations 6.7907077E-04 1.1856079E-02 at 180iterations finished qdiffx linear iterations at : 18:53:21 total time elapsed so far: 15.39000 # loops : 180 mean,max change (kT/e) : 6.7907077E-04 1.1856079E-02 energy calculations done at 15.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.57000 DelPhi exited at 18:53:22 15.568u 0.312s 0:16.33 97.1% 0+0k 0+0io 0pf+0w