Sun Oct 9 02:33:17 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 Sun Oct 9 2011 at 02:33:17 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2060 !!! WARNING: MG2 213 has a net charge of 1.4000 !!! WARNING: SAM 214 has a net charge of -0.6000 !!! WARNING: SAM 1 has a net charge of -0.5000 !!! WARNING: SAM 3 has a net charge of 0.4200 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7509440 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): -43.11300 0.4280000 ymin,ymax (A): -19.22700 28.18000 zmin,zma (A): -38.64100 4.808000 x,y,z range (A): 43.54100 47.40700 43.44900 scale (grids/A): 0.7509440 object centre (A): -21.34250 4.476501 -16.91650 number of atom coordinates read : 2060 total number of charged atoms : 1946 net assigned charge : -4.279984 assigned positive charge : 308.6867 centred at (gu) : 88.75957 91.55037 90.99088 assigned negative charge : -312.9671 centred at (gu) : 88.78072 91.51389 90.97805 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 8122 nv = 96 ne = 84 npr = 42566 no. pairs analyzed = 42566 no. exposed pairs = 2249 no. arc points = 15434 no. surface atoms = 769 nbur = 1291 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 612 mr = 5149 m= 9 mr = 180 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 191 time to turn everything in is 0.1700000 number of dielectric boundary points 3414 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1117 ## 76 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8419 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.3877198E-08 -9.5755951E-08 midg,1,midg; midg,igrid,midg -1.0691814E-07 -6.6776039E-08 1,midg,midg; igrid,midg,midg -8.7169653E-08 -9.7953425E-08 gauss-seidel spectral radius is 0.9907441 estimated iterations to convergence 84 setup time was (sec) 0.3600000 now iterating at: 02:33:17 rms-change max change #iterations 0.2647212 37.07090 at 10iterations 3.7073191E-02 5.213551 at 20iterations 5.1458431E-03 0.6203480 at 30iterations 7.3045603E-04 8.4754944E-02 at 40iterations 1.0283344E-04 1.1978149E-02 at 50iterations finished qdiffx linear iterations at : 02:33:20 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 1.0283344E-04 1.1978149E-02 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 02:33:21 3.444u 0.193s 0:03.91 92.8% 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 Sun Oct 9 2011 at 02:33:21 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2060 !!! WARNING: MG2 213 has a net charge of 1.4000 !!! WARNING: SAM 214 has a net charge of -0.6000 !!! WARNING: SAM 1 has a net charge of -0.5000 !!! WARNING: SAM 3 has a net charge of 0.4200 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.252832 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): -43.11300 0.4280000 ymin,ymax (A): -19.22700 28.18000 zmin,zma (A): -38.64100 4.808000 x,y,z range (A): 43.54100 47.40700 43.44900 scale (grids/A): 2.252832 object centre (A): -21.34250 4.476501 -16.91650 number of atom coordinates read : 2060 total number of charged atoms : 1946 net assigned charge : -4.279984 assigned positive charge : 308.6867 centred at (gu) : 86.27880 94.65096 92.97232 assigned negative charge : -312.9671 centred at (gu) : 86.34229 94.54180 92.93412 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 85696 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15434 grid for indexing accessible points = 1.400000 m= 37307 mr = 63828 m= 9192 mr = 30321 m= 1232 mr = 7057 m= 43 mr = 913 m= 0 mr = 5 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 4820 time to turn everything in is 0.4300000 number of dielectric boundary points 31346 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 36 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 15515 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) : 0.7509440 object centre at (A) : -21.34250 4.476501 -16.91650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.2819437E-03 -3.8431618E-02 midg,1,midg; midg,igrid,midg 1.2768111E-02 -5.9416749E-02 1,midg,midg; igrid,midg,midg -3.5085429E-02 -2.0121567E-02 gauss-seidel spectral radius is 0.9989327 estimated iterations to convergence 242 setup time was (sec) 0.6700000 now iterating at: 02:33:22 rms-change max change #iterations 5.149492 229.2537 at 10iterations 2.639592 81.28018 at 20iterations 1.349692 38.65964 at 30iterations 0.6942582 21.93011 at 40iterations 0.3552135 10.02275 at 50iterations 0.1813019 5.191467 at 60iterations 9.3246043E-02 2.711037 at 70iterations 4.7895495E-02 1.370691 at 80iterations 2.4472678E-02 0.6498985 at 90iterations 1.2591139E-02 0.3706093 at 100iterations 6.4568641E-03 0.1745596 at 110iterations 3.3042505E-03 9.1766357E-02 at 120iterations finished qdiffx linear iterations at : 02:33:30 total time elapsed so far: 8.790000 # loops : 120 mean,max change (kT/e) : 3.3042505E-03 9.1766357E-02 energy calculations done at 8.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.920000 DelPhi exited at 02:33:30 8.918u 0.210s 0:09.43 96.7% 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 Sun Oct 9 2011 at 02:33:30 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2060 !!! WARNING: MG2 213 has a net charge of 1.4000 !!! WARNING: SAM 214 has a net charge of -0.6000 !!! WARNING: SAM 1 has a net charge of -0.5000 !!! WARNING: SAM 3 has a net charge of 0.4200 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.379248 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): -43.11300 0.4280000 ymin,ymax (A): -19.22700 28.18000 zmin,zma (A): -38.64100 4.808000 x,y,z range (A): 43.54100 47.40700 43.44900 scale (grids/A): 3.379248 object centre (A): -21.34250 4.476501 -16.91650 number of atom coordinates read : 2060 total number of charged atoms : 1946 net assigned charge : -4.279984 assigned positive charge : 308.6867 centred at (gu) : 84.41806 96.97634 94.45851 assigned negative charge : -312.9671 centred at (gu) : 84.51353 96.81272 94.40133 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 197484 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15434 grid for indexing accessible points = 1.400000 m= 112714 mr = 152454 m= 51750 mr = 97379 m= 18260 mr = 45182 m= 4855 mr = 15551 m= 854 mr = 4132 m= 46 mr = 682 m= 0 mr = 21 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 16548 time to turn everything in is 1.340000 number of dielectric boundary points 70562 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 15568 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) : 2.252832 object centre at (A) : -21.34250 4.476501 -16.91650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1468921 -0.2709181 midg,1,midg; midg,igrid,midg 0.2967587 -0.7124148 1,midg,midg; igrid,midg,midg -0.3768699 -0.1210112 gauss-seidel spectral radius is 0.9993096 estimated iterations to convergence 300 setup time was (sec) 1.590000 now iterating at: 02:33:32 rms-change max change #iterations 10.96021 295.8990 at 10iterations 6.450604 123.5417 at 20iterations 3.799888 71.30434 at 30iterations 2.228418 36.53900 at 40iterations 1.310629 19.78835 at 50iterations 0.7679183 12.48029 at 60iterations 0.4512500 6.954502 at 70iterations 0.2644516 4.190695 at 80iterations 0.1550331 2.572033 at 90iterations 9.1054216E-02 1.477074 at 100iterations 5.3389903E-02 0.8021698 at 110iterations 3.1363480E-02 0.4980621 at 120iterations 1.8372139E-02 0.2846370 at 130iterations 1.0802779E-02 0.1727037 at 140iterations 6.3486807E-03 9.4955444E-02 at 150iterations 3.7352003E-03 5.9367180E-02 at 160iterations 2.2073814E-03 4.3368995E-02 at 170iterations 1.3098210E-03 2.1869659E-02 at 180iterations finished qdiffx linear iterations at : 02:33:44 total time elapsed so far: 13.39000 # loops : 180 mean,max change (kT/e) : 1.3098210E-03 2.1869659E-02 energy calculations done at 13.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.52000 DelPhi exited at 02:33:44 13.519u 0.227s 0:14.03 97.8% 0+0k 0+0io 0pf+0w