Mon Oct 10 16:10:57 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 Mon Oct 10 2011 at 16:10:57 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4603 !!! WARNING: GLM 134 has a net charge of -0.0940 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: ZN8 840 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.5532933 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): 7.630000 62.86400 ymin,ymax (A): -29.63600 34.70600 zmin,zma (A): -29.29000 33.45100 x,y,z range (A): 55.23400 64.34200 62.74100 scale (grids/A): 0.5532933 object centre (A): 35.24700 2.535001 2.080501 number of atom coordinates read : 4603 total number of charged atoms : 4447 net assigned charge : 7.106019 assigned positive charge : 694.3224 centred at (gu) : 89.67463 89.91699 88.70718 assigned negative charge : -687.2203 centred at (gu) : 89.66388 89.88387 88.71458 start vw surface at 0.2200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 9034 nv = 96 ne = 84 npr = 94095 no. pairs analyzed = 94095 no. exposed pairs = 5677 no. arc points = 38502 no. surface atoms = 1916 nbur = 2687 mkacc time = 0.3100000 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 = 1.540000 m= 363 mr = 4933 m= 0 mr = 19 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6300000 number of dielectric boundary points 4445 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3925 ## 522 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 12023 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.3462338E-10 3.5937822E-10 midg,1,midg; midg,igrid,midg 1.4064452E-10 1.0081418E-09 1,midg,midg; igrid,midg,midg 4.7548382E-10 6.7498540E-10 gauss-seidel spectral radius is 0.9832733 estimated iterations to convergence 64 setup time was (sec) 0.9700000 now iterating at: 16:10:59 rms-change max change #iterations 9.9544920E-02 14.27508 at 10iterations 7.1521164E-03 1.003675 at 20iterations 6.7604188E-04 0.1197701 at 30iterations 1.7320897E-04 3.1377792E-02 at 40iterations 6.7218156E-05 9.8438263E-03 at 50iterations finished qdiffx linear iterations at : 16:11:02 total time elapsed so far: 4.640000 # loops : 50 mean,max change (kT/e) : 6.7218156E-05 9.8438263E-03 energy calculations done at 4.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.860000 DelPhi exited at 16:11:03 4.865u 0.402s 0:05.55 94.7% 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 16:11:03 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4603 !!! WARNING: GLM 134 has a net charge of -0.0940 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: ZN8 840 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: 1.659880 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): 7.630000 62.86400 ymin,ymax (A): -29.63600 34.70600 zmin,zma (A): -29.29000 33.45100 x,y,z range (A): 55.23400 64.34200 62.74100 scale (grids/A): 1.659880 object centre (A): 35.24700 2.535001 2.080501 number of atom coordinates read : 4603 total number of charged atoms : 4447 net assigned charge : 7.106019 assigned positive charge : 694.3224 centred at (gu) : 89.02265 89.74986 86.12041 assigned negative charge : -687.2203 centred at (gu) : 88.99133 89.65127 86.14333 start vw surface at 0.2000000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 101642 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38502 grid for indexing accessible points = 1.400000 m= 32946 mr = 71971 m= 3760 mr = 23031 m= 106 mr = 1905 m= 2 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 426 time to turn everything in is 1.000000 number of dielectric boundary points 41537 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 405 iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 34171 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) : 0.5532933 object centre at (A) : 35.24700 2.535001 2.080501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5322926E-02 8.2256523E-04 midg,1,midg; midg,igrid,midg 2.2484103E-02 8.2826614E-03 1,midg,midg; igrid,midg,midg 4.5357291E-03 4.5545502E-03 gauss-seidel spectral radius is 0.9984077 estimated iterations to convergence 199 setup time was (sec) 1.340000 now iterating at: 16:11:05 rms-change max change #iterations 4.417832 159.7894 at 10iterations 1.945660 57.98994 at 20iterations 0.8590036 25.84851 at 30iterations 0.3790575 10.47363 at 40iterations 0.1671696 4.933606 at 50iterations 7.3709220E-02 2.074863 at 60iterations 3.2618735E-02 0.8774843 at 70iterations 1.4398360E-02 0.4162998 at 80iterations 6.4039784E-03 0.2079523 at 90iterations 2.8803365E-03 8.0474854E-02 at 100iterations 1.3077831E-03 3.8728476E-02 at 110iterations 6.2607083E-04 1.9540787E-02 at 120iterations finished qdiffx linear iterations at : 16:11:15 total time elapsed so far: 11.27000 # loops : 120 mean,max change (kT/e) : 6.2607083E-04 1.9540787E-02 energy calculations done at 11.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.48000 DelPhi exited at 16:11:15 11.489u 0.493s 0:12.24 97.7% 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 16:11:15 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4603 !!! WARNING: GLM 134 has a net charge of -0.0940 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: ZN8 840 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.489820 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): 7.630000 62.86400 ymin,ymax (A): -29.63600 34.70600 zmin,zma (A): -29.29000 33.45100 x,y,z range (A): 55.23400 64.34200 62.74100 scale (grids/A): 2.489820 object centre (A): 35.24700 2.535001 2.080501 number of atom coordinates read : 4603 total number of charged atoms : 4447 net assigned charge : 7.106019 assigned positive charge : 694.3224 centred at (gu) : 88.53357 89.62429 84.18024 assigned negative charge : -687.2203 centred at (gu) : 88.48699 89.47678 84.21496 start vw surface at 0.2200000 fill in re-entrant regions at 0.8100000 boundary points on vw surface= 236376 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38502 grid for indexing accessible points = 1.400000 m= 113026 mr = 175850 m= 34015 mr = 90256 m= 5945 mr = 25877 m= 454 mr = 3890 m= 4 mr = 199 m= 0 mr = 0 time to grow re-entrant surface = 1.580000 no. cavity mid-points inaccessible to solvent = 1370 time to turn everything in is 2.560000 number of dielectric boundary points 93748 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 2.750000 number of grid points assigned charge 35547 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) : 1.659880 object centre at (A) : 35.24700 2.535001 2.080501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3980954 -4.9617719E-02 midg,1,midg; midg,igrid,midg 0.4531599 6.0679529E-02 1,midg,midg; igrid,midg,midg 7.2427288E-02 9.3808003E-02 gauss-seidel spectral radius is 0.9992427 estimated iterations to convergence 287 setup time was (sec) 2.980000 now iterating at: 16:11:19 rms-change max change #iterations 11.39321 339.3157 at 10iterations 6.736110 147.3339 at 20iterations 3.947243 85.92551 at 30iterations 2.303613 55.45957 at 40iterations 1.338516 30.31715 at 50iterations 0.7757906 13.93360 at 60iterations 0.4495845 8.079523 at 70iterations 0.2588803 4.612919 at 80iterations 0.1491089 2.952004 at 90iterations 8.5763559E-02 1.506857 at 100iterations 4.9294006E-02 0.8243065 at 110iterations 2.8332593E-02 0.4625049 at 120iterations 1.6281862E-02 0.2821061 at 130iterations 9.3659628E-03 0.1547699 at 140iterations 5.3958925E-03 9.2483521E-02 at 150iterations 3.1220845E-03 5.2472591E-02 at 160iterations 1.8226140E-03 3.1932831E-02 at 170iterations 1.0837053E-03 1.9412994E-02 at 180iterations finished qdiffx linear iterations at : 16:11:39 total time elapsed so far: 22.97000 # loops : 180 mean,max change (kT/e) : 1.0837053E-03 1.9412994E-02 energy calculations done at 22.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 23.17000 DelPhi exited at 16:11:39 23.179u 0.497s 0:23.96 98.7% 0+0k 0+0io 0pf+0w