Mon Oct 10 17:02:26 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 17:02:26 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2822 !!! WARNING: HIT 107 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: 0.6187968 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): -8.768001 48.76300 ymin,ymax (A): -9.517000 38.19000 zmin,zma (A): -1.165000 54.55300 x,y,z range (A): 57.53100 47.70700 55.71800 scale (grids/A): 0.6187968 object centre (A): 19.99750 14.33650 26.69400 number of atom coordinates read : 2822 total number of charged atoms : 2681 net assigned charge : -2.485975 assigned positive charge : 427.0042 centred at (gu) : 89.04240 89.64430 89.35932 assigned negative charge : -429.4912 centred at (gu) : 88.96958 89.59753 89.33259 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7368 nv = 96 ne = 84 npr = 55888 no. pairs analyzed = 55888 no. exposed pairs = 3722 no. arc points = 26645 no. surface atoms = 1252 nbur = 1570 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 398 mr = 3857 m= 1 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 19 time to turn everything in is 0.3300000 number of dielectric boundary points 3876 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2633 ## 271 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8976 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.3102197E-09 2.9866040E-11 midg,1,midg; midg,igrid,midg -5.6015357E-09 1.3396649E-09 1,midg,midg; igrid,midg,midg -8.7302556E-09 2.6322868E-09 gauss-seidel spectral radius is 0.9865049 estimated iterations to convergence 70 setup time was (sec) 0.6300000 now iterating at: 17:02:27 rms-change max change #iterations 0.1361175 20.28397 at 10iterations 1.2324021E-02 1.712346 at 20iterations 1.1312234E-03 0.1648655 at 30iterations 1.0574580E-04 1.5193939E-02 at 40iterations 1.0700980E-05 1.5840530E-03 at 50iterations finished qdiffx linear iterations at : 17:02:31 total time elapsed so far: 4.550000 # loops : 50 mean,max change (kT/e) : 1.0700980E-05 1.5840530E-03 energy calculations done at 4.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.720000 DelPhi exited at 17:02:32 4.726u 0.415s 0:06.34 80.9% 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 Mon Oct 10 2011 at 17:02:32 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2822 !!! WARNING: HIT 107 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.856390 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): -8.768001 48.76300 ymin,ymax (A): -9.517000 38.19000 zmin,zma (A): -1.165000 54.55300 x,y,z range (A): 57.53100 47.70700 55.71800 scale (grids/A): 1.856390 object centre (A): 19.99750 14.33650 26.69400 number of atom coordinates read : 2822 total number of charged atoms : 2681 net assigned charge : -2.485975 assigned positive charge : 427.0042 centred at (gu) : 87.12643 88.93233 88.07726 assigned negative charge : -429.4912 centred at (gu) : 86.90832 88.79216 87.99744 start vw surface at 0.1300000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 80039 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26645 grid for indexing accessible points = 1.400000 m= 27378 mr = 54189 m= 3924 mr = 19340 m= 178 mr = 2215 m= 2 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 349 time to turn everything in is 0.6500000 number of dielectric boundary points 35743 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 205 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 21043 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) : 0.6187968 object centre at (A) : 19.99750 14.33650 26.69400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2200882E-02 6.5889950E-03 midg,1,midg; midg,igrid,midg -1.6723059E-02 -2.3480882E-03 1,midg,midg; igrid,midg,midg -4.6039026E-02 3.0491598E-02 gauss-seidel spectral radius is 0.9985982 estimated iterations to convergence 212 setup time was (sec) 0.9500000 now iterating at: 17:02:33 rms-change max change #iterations 4.276322 208.4948 at 10iterations 1.981372 66.32008 at 20iterations 0.9155461 32.15211 at 30iterations 0.4235313 13.95936 at 40iterations 0.1963761 6.027955 at 50iterations 9.0817563E-02 2.854946 at 60iterations 4.2021837E-02 1.291321 at 70iterations 1.9508839E-02 0.6313286 at 80iterations 9.0385936E-03 0.2882080 at 90iterations 4.1850107E-03 0.1267700 at 100iterations 1.9420470E-03 6.0329437E-02 at 110iterations 9.0155820E-04 2.7771473E-02 at 120iterations finished qdiffx linear iterations at : 17:02:44 total time elapsed so far: 11.13000 # loops : 120 mean,max change (kT/e) : 9.0155820E-04 2.7771473E-02 energy calculations done at 11.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.29000 DelPhi exited at 17:02:44 11.297u 0.488s 0:12.32 95.5% 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 17:02:45 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2822 !!! WARNING: HIT 107 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: 2.784586 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): -8.768001 48.76300 ymin,ymax (A): -9.517000 38.19000 zmin,zma (A): -1.165000 54.55300 x,y,z range (A): 57.53100 47.70700 55.71800 scale (grids/A): 2.784586 object centre (A): 19.99750 14.33650 26.69400 number of atom coordinates read : 2822 total number of charged atoms : 2681 net assigned charge : -2.485975 assigned positive charge : 427.0042 centred at (gu) : 85.68943 88.39833 87.11566 assigned negative charge : -429.4912 centred at (gu) : 85.36250 88.18820 86.99612 start vw surface at 0.1200000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 184884 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26645 grid for indexing accessible points = 1.400000 m= 90227 mr = 131475 m= 30861 mr = 72404 m= 6859 mr = 23881 m= 801 mr = 4803 m= 27 mr = 410 m= 0 mr = 5 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 1082 time to turn everything in is 1.680000 number of dielectric boundary points 80681 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.820000 number of grid points assigned charge 21446 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) : 1.856390 object centre at (A) : 19.99750 14.33650 26.69400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1965651 -0.1777579 midg,1,midg; midg,igrid,midg -0.1407449 -4.9423505E-02 1,midg,midg; igrid,midg,midg -0.5613550 0.4611735 gauss-seidel spectral radius is 0.9992692 estimated iterations to convergence 292 setup time was (sec) 2.030000 now iterating at: 17:02:47 rms-change max change #iterations 10.43682 313.2352 at 10iterations 6.187469 156.6903 at 20iterations 3.643283 84.07455 at 30iterations 2.128430 47.59009 at 40iterations 1.242620 23.56302 at 50iterations 0.7228167 13.98995 at 60iterations 0.4195679 8.206746 at 70iterations 0.2432733 5.033133 at 80iterations 0.1408968 2.727093 at 90iterations 8.1284225E-02 1.530111 at 100iterations 4.7075741E-02 0.9154568 at 110iterations 2.7180426E-02 0.5043964 at 120iterations 1.5689798E-02 0.3141060 at 130iterations 9.0524768E-03 0.1747227 at 140iterations 5.2124728E-03 9.0932846E-02 at 150iterations 3.0104525E-03 5.4004669E-02 at 160iterations 1.7342052E-03 3.0742645E-02 at 170iterations 1.0002641E-03 1.8607140E-02 at 180iterations finished qdiffx linear iterations at : 17:03:04 total time elapsed so far: 18.77000 # loops : 180 mean,max change (kT/e) : 1.0002641E-03 1.8607140E-02 energy calculations done at 18.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.94000 DelPhi exited at 17:03:05 18.941u 0.494s 0:19.93 97.4% 0+0k 0+0io 0pf+0w