Mon Oct 10 14:00:16 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+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 Mon Oct 10 2011 at 14:00:16 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2589 !!! 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: ZN4 475 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: 0.6287420 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): -31.91200 17.48800 ymin,ymax (A): -24.01900 23.00700 zmin,zma (A): -12.36000 44.26100 x,y,z range (A): 49.40000 47.02600 56.62100 scale (grids/A): 0.6287420 object centre (A): -7.212000 -0.5059996 15.95050 number of atom coordinates read : 2589 total number of charged atoms : 2457 net assigned charge : 4.000009 assigned positive charge : 391.9970 centred at (gu) : 88.50302 89.27694 89.88636 assigned negative charge : -387.9975 centred at (gu) : 88.41663 89.32275 89.78692 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6765 nv = 96 ne = 84 npr = 53633 no. pairs analyzed = 53633 no. exposed pairs = 2998 no. arc points = 21738 no. surface atoms = 1009 nbur = 1580 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 376 mr = 3846 m= 3 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 31 time to turn everything in is 0.2900000 number of dielectric boundary points 3239 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2127 ## 221 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8270 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.3799626E-09 1.2351299E-08 midg,1,midg; midg,igrid,midg 9.5550661E-09 3.4868131E-10 1,midg,midg; igrid,midg,midg -4.4848649E-09 8.3822327E-09 gauss-seidel spectral radius is 0.9868938 estimated iterations to convergence 71 setup time was (sec) 0.5100000 now iterating at: 14:00:17 rms-change max change #iterations 0.1358232 20.74514 at 10iterations 1.2920438E-02 1.967463 at 20iterations 1.2537683E-03 0.1984596 at 30iterations 1.1800237E-04 1.4837265E-02 at 40iterations 1.1392807E-05 1.5926361E-03 at 50iterations finished qdiffx linear iterations at : 14:00:19 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 1.1392807E-05 1.5926361E-03 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.140000 DelPhi exited at 14:00:21 3.144u 0.152s 0:04.72 69.7% 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 14:00:21 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2589 !!! 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: ZN4 475 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.886226 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): -31.91200 17.48800 ymin,ymax (A): -24.01900 23.00700 zmin,zma (A): -12.36000 44.26100 x,y,z range (A): 49.40000 47.02600 56.62100 scale (grids/A): 1.886226 object centre (A): -7.212000 -0.5059996 15.95050 number of atom coordinates read : 2589 total number of charged atoms : 2457 net assigned charge : 4.000009 assigned positive charge : 391.9970 centred at (gu) : 85.50863 87.83054 89.65846 assigned negative charge : -387.9975 centred at (gu) : 85.24963 87.96790 89.36056 start vw surface at 0.1800000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 73453 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21738 grid for indexing accessible points = 1.400000 m= 26361 mr = 51554 m= 4154 mr = 19877 m= 252 mr = 2694 m= 6 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 4173 time to turn everything in is 0.5400000 number of dielectric boundary points 29995 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 160 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 19316 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) : 0.6287420 object centre at (A) : -7.212000 -0.5059996 15.95050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8214272E-02 2.2034978E-02 midg,1,midg; midg,igrid,midg 1.2540119E-02 1.7613899E-03 1,midg,midg; igrid,midg,midg -1.5815565E-03 3.0253485E-02 gauss-seidel spectral radius is 0.9986060 estimated iterations to convergence 212 setup time was (sec) 0.8000000 now iterating at: 14:00:22 rms-change max change #iterations 4.127667 171.1441 at 10iterations 1.924013 74.93654 at 20iterations 0.8936117 30.18165 at 30iterations 0.4147075 13.25053 at 40iterations 0.1931113 6.037338 at 50iterations 8.9611471E-02 2.801811 at 60iterations 4.1531596E-02 1.323021 at 70iterations 1.9342605E-02 0.7253323 at 80iterations 9.0021659E-03 0.3017218 at 90iterations 4.1654846E-03 0.1275291 at 100iterations 1.9445010E-03 6.5876007E-02 at 110iterations 9.0542191E-04 2.8060913E-02 at 120iterations finished qdiffx linear iterations at : 14:00:28 total time elapsed so far: 6.770000 # loops : 120 mean,max change (kT/e) : 9.0542191E-04 2.8060913E-02 energy calculations done at 6.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.950000 DelPhi exited at 14:00:30 6.950u 0.163s 0:09.20 77.2% 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 Mon Oct 10 2011 at 14:00:31 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2589 !!! 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: ZN4 475 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.829339 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): -31.91200 17.48800 ymin,ymax (A): -24.01900 23.00700 zmin,zma (A): -12.36000 44.26100 x,y,z range (A): 49.40000 47.02600 56.62100 scale (grids/A): 2.829339 object centre (A): -7.212000 -0.5059996 15.95050 number of atom coordinates read : 2589 total number of charged atoms : 2457 net assigned charge : 4.000009 assigned positive charge : 391.9970 centred at (gu) : 83.26282 86.74551 89.48764 assigned negative charge : -387.9975 centred at (gu) : 82.87451 86.95177 89.04069 start vw surface at 0.2400000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 169528 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21738 grid for indexing accessible points = 1.400000 m= 86649 mr = 124379 m= 31006 mr = 72070 m= 7413 mr = 25201 m= 1069 mr = 5724 m= 83 mr = 732 m= 1 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 13962 time to turn everything in is 1.390000 number of dielectric boundary points 67594 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 19652 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) : 1.886226 object centre at (A) : -7.212000 -0.5059996 15.95050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1539892 0.2057600 midg,1,midg; midg,igrid,midg 0.1297769 1.9188683E-02 1,midg,midg; igrid,midg,midg -9.6562719E-03 0.3773432 gauss-seidel spectral radius is 0.9992444 estimated iterations to convergence 287 setup time was (sec) 1.710000 now iterating at: 14:00:33 rms-change max change #iterations 9.632877 302.6971 at 10iterations 5.545378 122.2401 at 20iterations 3.171157 58.34262 at 30iterations 1.814524 34.30502 at 40iterations 1.035496 18.28893 at 50iterations 0.5912930 12.19511 at 60iterations 0.3373911 6.601497 at 70iterations 0.1931445 3.614685 at 80iterations 0.1100735 2.018405 at 90iterations 6.2779099E-02 1.230011 at 100iterations 3.5852734E-02 0.6431046 at 110iterations 2.0432100E-02 0.3791809 at 120iterations 1.1662117E-02 0.2291050 at 130iterations 6.6591473E-03 0.1304770 at 140iterations 3.7953951E-03 6.7512512E-02 at 150iterations 2.1646782E-03 4.2865753E-02 at 160iterations 1.2348450E-03 2.3244858E-02 at 170iterations 7.0467661E-04 1.3410568E-02 at 180iterations finished qdiffx linear iterations at : 14:00:44 total time elapsed so far: 12.48000 # loops : 180 mean,max change (kT/e) : 7.0467661E-04 1.3410568E-02 energy calculations done at 12.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.65000 DelPhi exited at 14:00:45 12.650u 0.251s 0:14.22 90.7% 0+0k 0+0io 0pf+0w