Sat Oct 8 20:05:02 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 Sat Oct 8 2011 at 20:05:02 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2619 !!! 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 765 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6225299 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): -32.14300 17.47900 ymin,ymax (A): -23.51600 23.67300 zmin,zma (A): -12.30200 44.88400 x,y,z range (A): 49.62200 47.18900 57.18600 scale (grids/A): 0.6225299 object centre (A): -7.331999 7.8500748E-02 16.29100 number of atom coordinates read : 2619 total number of charged atoms : 2475 net assigned charge : 3.500007 assigned positive charge : 397.0500 centred at (gu) : 88.77794 89.02054 89.62447 assigned negative charge : -393.5505 centred at (gu) : 88.68147 89.08177 89.51799 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6566 nv = 96 ne = 84 npr = 54877 no. pairs analyzed = 54877 no. exposed pairs = 3038 no. arc points = 21591 no. surface atoms = 1023 nbur = 1596 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 306 mr = 3650 m= 3 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 36 time to turn everything in is 0.3000000 number of dielectric boundary points 3197 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2191 ## 244 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8256 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.0946154E-09 9.8842712E-09 midg,1,midg; midg,igrid,midg 9.3345145E-09 -1.0449385E-09 1,midg,midg; igrid,midg,midg -5.2344693E-09 7.6776843E-09 gauss-seidel spectral radius is 0.9866335 estimated iterations to convergence 71 setup time was (sec) 0.5900000 now iterating at: 20:05:03 rms-change max change #iterations 0.1308870 21.41668 at 10iterations 1.2284758E-02 1.713814 at 20iterations 1.1453573E-03 0.1772556 at 30iterations 1.0713087E-04 1.8201828E-02 at 40iterations 9.9391782E-06 1.3656616E-03 at 50iterations finished qdiffx linear iterations at : 20:05:06 total time elapsed so far: 4.130000 # loops : 50 mean,max change (kT/e) : 9.9391782E-06 1.3656616E-03 energy calculations done at 4.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.300000 DelPhi exited at 20:05:07 4.308u 0.285s 0:04.86 94.2% 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 Sat Oct 8 2011 at 20:05:07 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2619 !!! 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 765 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.867590 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): -32.14300 17.47900 ymin,ymax (A): -23.51600 23.67300 zmin,zma (A): -12.30200 44.88400 x,y,z range (A): 49.62200 47.18900 57.18600 scale (grids/A): 1.867590 object centre (A): -7.331999 7.8500748E-02 16.29100 number of atom coordinates read : 2619 total number of charged atoms : 2475 net assigned charge : 3.500007 assigned positive charge : 397.0500 centred at (gu) : 86.33323 87.06123 88.87304 assigned negative charge : -393.5505 centred at (gu) : 86.04416 87.24493 88.55399 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 72095 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21591 grid for indexing accessible points = 1.400000 m= 24090 mr = 50313 m= 3287 mr = 17736 m= 152 mr = 2001 m= 1 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 5043 time to turn everything in is 0.5600000 number of dielectric boundary points 29530 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 168 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 19415 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) : 0.6225299 object centre at (A) : -7.331999 7.8500748E-02 16.29100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2721037E-02 2.6377168E-02 midg,1,midg; midg,igrid,midg 1.5400513E-02 1.4768353E-03 1,midg,midg; igrid,midg,midg -4.9642911E-03 3.3011422E-02 gauss-seidel spectral radius is 0.9985814 estimated iterations to convergence 210 setup time was (sec) 0.9000000 now iterating at: 20:05:08 rms-change max change #iterations 4.110907 186.4158 at 10iterations 1.892511 70.22004 at 20iterations 0.8714285 30.46630 at 30iterations 0.4030694 12.80805 at 40iterations 0.1862810 5.773325 at 50iterations 8.5656889E-02 2.826667 at 60iterations 3.9810456E-02 1.381057 at 70iterations 1.8308792E-02 0.5478764 at 80iterations 8.4587857E-03 0.2659740 at 90iterations 3.9034502E-03 0.1255407 at 100iterations 1.8045050E-03 6.6139221E-02 at 110iterations 8.3364133E-04 2.8708458E-02 at 120iterations finished qdiffx linear iterations at : 20:05:17 total time elapsed so far: 9.820000 # loops : 120 mean,max change (kT/e) : 8.3364133E-04 2.8708458E-02 energy calculations done at 9.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.00000 DelPhi exited at 20:05:17 10.000u 0.310s 0:10.57 97.5% 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 20:05:17 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2619 !!! 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 765 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.801385 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): -32.14300 17.47900 ymin,ymax (A): -23.51600 23.67300 zmin,zma (A): -12.30200 44.88400 x,y,z range (A): 49.62200 47.18900 57.18600 scale (grids/A): 2.801385 object centre (A): -7.331999 7.8500748E-02 16.29100 number of atom coordinates read : 2619 total number of charged atoms : 2475 net assigned charge : 3.500007 assigned positive charge : 397.0500 centred at (gu) : 84.49953 85.59174 88.30934 assigned negative charge : -393.5505 centred at (gu) : 84.06629 85.86729 87.83092 start vw surface at 0.1400000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 167000 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21591 grid for indexing accessible points = 1.400000 m= 81303 mr = 122147 m= 26551 mr = 66551 m= 5719 mr = 21165 m= 689 mr = 4285 m= 28 mr = 449 m= 0 mr = 11 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 17248 time to turn everything in is 1.390000 number of dielectric boundary points 66682 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.550000 number of grid points assigned charge 19797 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) : 1.867590 object centre at (A) : -7.331999 7.8500748E-02 16.29100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0802260E-02 0.3482476 midg,1,midg; midg,igrid,midg 0.1777295 5.2681606E-02 1,midg,midg; igrid,midg,midg -3.6490534E-02 0.4131709 gauss-seidel spectral radius is 0.9992383 estimated iterations to convergence 286 setup time was (sec) 1.760000 now iterating at: 20:05:19 rms-change max change #iterations 9.639771 444.4515 at 10iterations 5.553406 142.7314 at 20iterations 3.172159 70.81081 at 30iterations 1.809517 36.96947 at 40iterations 1.037341 23.43321 at 50iterations 0.5903966 11.54350 at 60iterations 0.3370916 6.727844 at 70iterations 0.1922258 3.947206 at 80iterations 0.1097052 1.991980 at 90iterations 6.2375810E-02 1.210562 at 100iterations 3.5531458E-02 0.7127323 at 110iterations 2.0265086E-02 0.3755894 at 120iterations 1.1538645E-02 0.2153931 at 130iterations 6.5720910E-03 0.1246243 at 140iterations 3.7412331E-03 7.4581146E-02 at 150iterations 2.1307801E-03 3.8650513E-02 at 160iterations 1.2129222E-03 2.2705078E-02 at 170iterations 6.9266034E-04 1.3062477E-02 at 180iterations finished qdiffx linear iterations at : 20:05:33 total time elapsed so far: 15.80000 # loops : 180 mean,max change (kT/e) : 6.9266034E-04 1.3062477E-02 energy calculations done at 15.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.98000 DelPhi exited at 20:05:34 15.984u 0.339s 0:16.59 98.3% 0+0k 0+0io 0pf+0w