Sat Oct 15 14:14:29 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 15 2011 at 14:14:29 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4674 !!! WARNING: GLM 172 has a net charge of -0.0940 !!! WARNING: HEM 810 has a net charge of 1.4000 !!! WARNING: ZN8 811 has a net charge of 1.4000 !!! WARNING: FE 3 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5228681 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): -24.24200 40.39100 ymin,ymax (A): -18.12300 46.91000 zmin,zma (A): 7.018000 75.10400 x,y,z range (A): 64.63300 65.03300 68.08601 scale (grids/A): 0.5228681 object centre (A): 8.074502 14.39350 41.06100 number of atom coordinates read : 4674 total number of charged atoms : 4430 net assigned charge : 10.10603 assigned positive charge : 710.1817 centred at (gu) : 91.19282 88.55734 87.81833 assigned negative charge : -700.0795 centred at (gu) : 91.29167 88.68928 87.66531 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8192 nv = 96 ne = 84 npr = 92837 no. pairs analyzed = 92837 no. exposed pairs = 6152 no. arc points = 42575 no. surface atoms = 2058 nbur = 2616 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 331 mr = 4187 m= 0 mr = 7 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 4329 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4143 ## 598 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 10828 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.2397033E-10 5.0714538E-10 midg,1,midg; midg,igrid,midg 1.1642416E-09 -2.0843170E-10 1,midg,midg; igrid,midg,midg 4.9021143E-10 -2.2985336E-10 gauss-seidel spectral radius is 0.9812885 estimated iterations to convergence 60 setup time was (sec) 0.5400000 now iterating at: 14:14:30 rms-change max change #iterations 7.5593323E-02 11.54437 at 10iterations 5.4904642E-03 0.7761326 at 20iterations 1.3762944E-03 0.1987534 at 30iterations 5.9916836E-04 8.6184502E-02 at 40iterations 2.6780728E-04 3.8230896E-02 at 50iterations finished qdiffx linear iterations at : 14:14:33 total time elapsed so far: 3.950000 # loops : 50 mean,max change (kT/e) : 2.6780728E-04 3.8230896E-02 energy calculations done at 3.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.080000 DelPhi exited at 14:14:34 4.082u 0.262s 0:04.73 91.7% 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 Sat Oct 15 2011 at 14:14:34 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4674 !!! WARNING: GLM 172 has a net charge of -0.0940 !!! WARNING: HEM 810 has a net charge of 1.4000 !!! WARNING: ZN8 811 has a net charge of 1.4000 !!! WARNING: FE 3 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.568604 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): -24.24200 40.39100 ymin,ymax (A): -18.12300 46.91000 zmin,zma (A): 7.018000 75.10400 x,y,z range (A): 64.63300 65.03300 68.08601 scale (grids/A): 1.568604 object centre (A): 8.074502 14.39350 41.06100 number of atom coordinates read : 4674 total number of charged atoms : 4430 net assigned charge : 10.10603 assigned positive charge : 710.1817 centred at (gu) : 93.57676 85.67082 83.45396 assigned negative charge : -700.0795 centred at (gu) : 93.87457 86.06773 82.99580 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 92490 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42575 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 27261 mr = 62861 m= 2536 mr = 18038 m= 57 mr = 1083 m= 0 mr = 6 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 133 time to turn everything in is 0.4700000 number of dielectric boundary points 40356 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 482 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 33477 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) : 0.5228681 object centre at (A) : 8.074502 14.39350 41.06100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.0029590E-03 2.3678172E-02 midg,1,midg; midg,igrid,midg 1.2972630E-02 -9.8963110E-03 1,midg,midg; igrid,midg,midg 1.4812691E-02 4.4974978E-03 gauss-seidel spectral radius is 0.9982051 estimated iterations to convergence 187 setup time was (sec) 0.7300000 now iterating at: 14:14:35 rms-change max change #iterations 3.990361 144.7337 at 10iterations 1.672287 54.34005 at 20iterations 0.7006598 22.50227 at 30iterations 0.2944609 9.024174 at 40iterations 0.1234019 3.825477 at 50iterations 5.2132193E-02 1.592300 at 60iterations 2.2065161E-02 0.7370453 at 70iterations 9.6028466E-03 0.3220339 at 80iterations 4.4424091E-03 0.1378994 at 90iterations 2.3148353E-03 8.6402893E-02 at 100iterations 1.4120196E-03 4.8547745E-02 at 110iterations 9.7126345E-04 3.3832550E-02 at 120iterations finished qdiffx linear iterations at : 14:14:44 total time elapsed so far: 9.350000 # loops : 120 mean,max change (kT/e) : 9.7126345E-04 3.3832550E-02 energy calculations done at 9.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.490000 DelPhi exited at 14:14:44 9.490u 0.304s 0:10.44 93.7% 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 Sat Oct 15 2011 at 14:14:44 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4674 !!! WARNING: GLM 172 has a net charge of -0.0940 !!! WARNING: HEM 810 has a net charge of 1.4000 !!! WARNING: ZN8 811 has a net charge of 1.4000 !!! WARNING: FE 3 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.352906 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): -24.24200 40.39100 ymin,ymax (A): -18.12300 46.91000 zmin,zma (A): 7.018000 75.10400 x,y,z range (A): 64.63300 65.03300 68.08601 scale (grids/A): 2.352906 object centre (A): 8.074502 14.39350 41.06100 number of atom coordinates read : 4674 total number of charged atoms : 4430 net assigned charge : 10.10603 assigned positive charge : 710.1817 centred at (gu) : 95.36473 83.50594 80.18061 assigned negative charge : -700.0795 centred at (gu) : 95.81185 84.10149 79.49355 start vw surface at 0.1100000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 215209 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42575 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 96753 mr = 154338 m= 25188 mr = 75246 m= 3700 mr = 17943 m= 215 mr = 2308 m= 5 mr = 82 m= 0 mr = 0 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 394 time to turn everything in is 1.180000 number of dielectric boundary points 91153 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 56 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 35368 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) : 1.568604 object centre at (A) : 8.074502 14.39350 41.06100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5834718 0.5260750 midg,1,midg; midg,igrid,midg 0.1574401 -0.1915631 1,midg,midg; igrid,midg,midg 0.2718268 9.6488550E-02 gauss-seidel spectral radius is 0.9991886 estimated iterations to convergence 277 setup time was (sec) 1.520000 now iterating at: 14:14:47 rms-change max change #iterations 10.61027 309.4326 at 10iterations 6.123288 183.3745 at 20iterations 3.513484 72.97585 at 30iterations 2.006993 42.78687 at 40iterations 1.138210 23.94763 at 50iterations 0.6448560 13.64568 at 60iterations 0.3650962 8.052006 at 70iterations 0.2059235 4.381493 at 80iterations 0.1162493 2.514360 at 90iterations 6.5342121E-02 1.261927 at 100iterations 3.6748841E-02 0.6805477 at 110iterations 2.0714877E-02 0.3846779 at 120iterations 1.1622087E-02 0.2102814 at 130iterations 6.5439618E-03 0.1232212 at 140iterations 3.6970824E-03 7.1664810E-02 at 150iterations 2.0962588E-03 4.0824890E-02 at 160iterations 1.2053850E-03 2.3257732E-02 at 170iterations 7.0982345E-04 1.8362045E-02 at 180iterations finished qdiffx linear iterations at : 14:15:02 total time elapsed so far: 15.98000 # loops : 180 mean,max change (kT/e) : 7.0982345E-04 1.8362045E-02 energy calculations done at 15.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.11000 DelPhi exited at 14:15:02 16.112u 0.339s 0:18.05 91.0% 0+0k 0+0io 0pf+0w