Sat Oct 8 19:50:27 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 19:50:27 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2621 !!! 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: ZN7 729 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6142272 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): -32.14400 17.69900 ymin,ymax (A): -23.52500 22.88600 zmin,zma (A): -12.56800 45.39100 x,y,z range (A): 49.84300 46.41100 57.95900 scale (grids/A): 0.6142272 object centre (A): -7.222501 -0.3195000 16.41150 number of atom coordinates read : 2621 total number of charged atoms : 2475 net assigned charge : 3.500007 assigned positive charge : 395.4500 centred at (gu) : 88.70792 89.28122 89.62903 assigned negative charge : -391.9505 centred at (gu) : 88.60858 89.34729 89.52063 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6424 nv = 96 ne = 84 npr = 54921 no. pairs analyzed = 54921 no. exposed pairs = 3028 no. arc points = 21753 no. surface atoms = 1012 nbur = 1609 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 313 mr = 3548 m= 2 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 95 time to turn everything in is 0.2000000 number of dielectric boundary points 3154 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2241 ## 237 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8050 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.1102517E-09 7.8199891E-09 midg,1,midg; midg,igrid,midg 7.2143007E-09 -1.1106833E-09 1,midg,midg; igrid,midg,midg -4.4057025E-09 6.0059513E-09 gauss-seidel spectral radius is 0.9862738 estimated iterations to convergence 70 setup time was (sec) 0.3900000 now iterating at: 19:50:28 rms-change max change #iterations 0.1188108 18.06735 at 10iterations 1.0681164E-02 1.507050 at 20iterations 9.5665874E-04 0.1502924 at 30iterations 8.8396198E-05 1.3092041E-02 at 40iterations 7.9085667E-06 1.0957718E-03 at 50iterations finished qdiffx linear iterations at : 19:50:30 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 7.9085667E-06 1.0957718E-03 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 19:50:31 3.493u 0.195s 0:04.00 92.0% 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 Sat Oct 8 2011 at 19:50:31 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2621 !!! 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: ZN7 729 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.842682 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): -32.14400 17.69900 ymin,ymax (A): -23.52500 22.88600 zmin,zma (A): -12.56800 45.39100 x,y,z range (A): 49.84300 46.41100 57.95900 scale (grids/A): 1.842682 object centre (A): -7.222501 -0.3195000 16.41150 number of atom coordinates read : 2621 total number of charged atoms : 2475 net assigned charge : 3.500007 assigned positive charge : 395.4500 centred at (gu) : 86.12343 87.84328 88.88652 assigned negative charge : -391.9505 centred at (gu) : 85.82545 88.04165 88.56179 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 70484 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21753 grid for indexing accessible points = 1.400000 m= 24094 mr = 49291 m= 3235 mr = 17652 m= 146 mr = 1971 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 6365 time to turn everything in is 0.3500000 number of dielectric boundary points 29010 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 219 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 19418 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) : 0.6142272 object centre at (A) : -7.222501 -0.3195000 16.41150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3503017E-02 2.7137013E-02 midg,1,midg; midg,igrid,midg 1.3116292E-02 -2.7920415E-03 1,midg,midg; igrid,midg,midg -5.2424553E-03 3.2747384E-02 gauss-seidel spectral radius is 0.9985448 estimated iterations to convergence 208 setup time was (sec) 0.6000000 now iterating at: 19:50:32 rms-change max change #iterations 3.986537 158.1367 at 10iterations 1.820067 64.69210 at 20iterations 0.8334050 28.39635 at 30iterations 0.3804395 13.67641 at 40iterations 0.1738997 5.870913 at 50iterations 7.9682209E-02 2.695522 at 60iterations 3.6422856E-02 1.155118 at 70iterations 1.6636817E-02 0.5030098 at 80iterations 7.5979228E-03 0.2439880 at 90iterations 3.4733734E-03 0.1169801 at 100iterations 1.5944861E-03 5.2604675E-02 at 110iterations 7.2698772E-04 2.4799824E-02 at 120iterations finished qdiffx linear iterations at : 19:50:40 total time elapsed so far: 8.390000 # loops : 120 mean,max change (kT/e) : 7.2698772E-04 2.4799824E-02 energy calculations done at 8.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.520000 DelPhi exited at 19:50:40 8.520u 0.240s 0:09.07 96.5% 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 Sat Oct 8 2011 at 19:50:40 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2621 !!! 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: ZN7 729 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.764023 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): -32.14400 17.69900 ymin,ymax (A): -23.52500 22.88600 zmin,zma (A): -12.56800 45.39100 x,y,z range (A): 49.84300 46.41100 57.95900 scale (grids/A): 2.764023 object centre (A): -7.222501 -0.3195000 16.41150 number of atom coordinates read : 2621 total number of charged atoms : 2475 net assigned charge : 3.500007 assigned positive charge : 395.4500 centred at (gu) : 84.18498 86.76466 88.32983 assigned negative charge : -391.9505 centred at (gu) : 83.73812 87.06244 87.84248 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 163292 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21753 grid for indexing accessible points = 1.400000 m= 80055 mr = 119327 m= 26226 mr = 65653 m= 5464 mr = 20802 m= 630 mr = 4043 m= 16 mr = 417 m= 0 mr = 3 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 21450 time to turn everything in is 0.8900000 number of dielectric boundary points 65438 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 19794 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) : 1.842682 object centre at (A) : -7.222501 -0.3195000 16.41150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.2285366E-02 0.3740333 midg,1,midg; midg,igrid,midg 0.1553364 -3.4277335E-02 1,midg,midg; igrid,midg,midg -5.0684419E-02 0.4364265 gauss-seidel spectral radius is 0.9992287 estimated iterations to convergence 284 setup time was (sec) 1.150000 now iterating at: 19:50:42 rms-change max change #iterations 9.423844 258.7576 at 10iterations 5.410486 113.4159 at 20iterations 3.092208 71.69842 at 30iterations 1.761056 38.75881 at 40iterations 1.004311 21.22927 at 50iterations 0.5715884 13.83105 at 60iterations 0.3245842 7.179702 at 70iterations 0.1843211 3.828262 at 80iterations 0.1049780 1.957940 at 90iterations 5.9491314E-02 1.087317 at 100iterations 3.3770457E-02 0.6777725 at 110iterations 1.9173639E-02 0.3819313 at 120iterations 1.0875245E-02 0.2093220 at 130iterations 6.1858436E-03 0.1269665 at 140iterations 3.5020940E-03 6.2491417E-02 at 150iterations 1.9891718E-03 4.1912079E-02 at 160iterations 1.1289319E-03 1.9176483E-02 at 170iterations 6.3957815E-04 1.2292862E-02 at 180iterations finished qdiffx linear iterations at : 19:50:54 total time elapsed so far: 13.71000 # loops : 180 mean,max change (kT/e) : 6.3957815E-04 1.2292862E-02 energy calculations done at 13.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.85000 DelPhi exited at 19:50:55 13.849u 0.266s 0:14.39 97.9% 0+0k 0+0io 0pf+0w