Mon Oct 10 19:33:10 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 19:33:10 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: 334 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3071 !!! WARNING: HIT 107 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5562674 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): -29.58200 34.41600 ymin,ymax (A): -21.59900 25.78700 zmin,zma (A): -7.154000 39.02300 x,y,z range (A): 63.99800 47.38600 46.17700 scale (grids/A): 0.5562674 object centre (A): 2.417001 2.094000 15.93450 number of atom coordinates read : 3071 total number of charged atoms : 2930 net assigned charge : -0.4859794 assigned positive charge : 467.4518 centred at (gu) : 90.42786 90.13615 89.75036 assigned negative charge : -467.9389 centred at (gu) : 90.45782 89.97491 89.65257 start vw surface at 0.2000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 6040 nv = 96 ne = 84 npr = 61981 no. pairs analyzed = 61981 no. exposed pairs = 3978 no. arc points = 27806 no. surface atoms = 1341 nbur = 1730 mkacc time = 0.1300000 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= 238 mr = 3016 m= 0 mr = 11 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3251 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2824 ## 343 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 7949 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1190286E-09 8.8863933E-10 midg,1,midg; midg,igrid,midg -1.6638080E-09 1.6266110E-09 1,midg,midg; igrid,midg,midg 2.3694344E-10 -3.8707093E-10 gauss-seidel spectral radius is 0.9833397 estimated iterations to convergence 64 setup time was (sec) 0.6000000 now iterating at: 19:33:11 rms-change max change #iterations 8.3976701E-02 12.85813 at 10iterations 5.7377960E-03 1.347568 at 20iterations 4.0329102E-04 6.4338684E-02 at 30iterations 2.9652609E-05 5.1155090E-03 at 40iterations 2.2856279E-06 3.1566620E-04 at 50iterations finished qdiffx linear iterations at : 19:33:13 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 2.2856279E-06 3.1566620E-04 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 19:33:14 3.372u 0.208s 0:04.12 86.6% 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 19:33:14 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: 334 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3071 !!! WARNING: HIT 107 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.668802 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): -29.58200 34.41600 ymin,ymax (A): -21.59900 25.78700 zmin,zma (A): -7.154000 39.02300 x,y,z range (A): 63.99800 47.38600 46.17700 scale (grids/A): 1.668802 object centre (A): 2.417001 2.094000 15.93450 number of atom coordinates read : 3071 total number of charged atoms : 2930 net assigned charge : -0.4859794 assigned positive charge : 467.4518 centred at (gu) : 91.28249 90.40782 89.25043 assigned negative charge : -467.9389 centred at (gu) : 91.37317 89.92458 88.95743 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 66913 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27806 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 19892 mr = 44474 m= 2124 mr = 13247 m= 64 mr = 1058 m= 0 mr = 3 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 35 time to turn everything in is 0.4800000 number of dielectric boundary points 30211 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 322 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 22538 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) : 0.5562674 object centre at (A) : 2.417001 2.094000 15.93450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.7728070E-03 5.7524228E-03 midg,1,midg; midg,igrid,midg -1.8468101E-02 1.1162729E-02 1,midg,midg; igrid,midg,midg -1.4559547E-02 -1.4442419E-02 gauss-seidel spectral radius is 0.9982715 estimated iterations to convergence 191 setup time was (sec) 0.7800000 now iterating at: 19:33:15 rms-change max change #iterations 3.620961 170.2207 at 10iterations 1.539310 54.20388 at 20iterations 0.6530998 23.78304 at 30iterations 0.2769792 9.402855 at 40iterations 0.1185920 4.394445 at 50iterations 5.0187610E-02 2.075550 at 60iterations 2.1363128E-02 0.8913879 at 70iterations 9.0995776E-03 0.3101377 at 80iterations 3.8763706E-03 0.1389885 at 90iterations 1.6544225E-03 6.6902161E-02 at 100iterations 7.0439524E-04 2.4669647E-02 at 110iterations 3.0066990E-04 1.1198997E-02 at 120iterations finished qdiffx linear iterations at : 19:33:22 total time elapsed so far: 7.310000 # loops : 120 mean,max change (kT/e) : 3.0066990E-04 1.1198997E-02 energy calculations done at 7.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.490000 DelPhi exited at 19:33:22 7.488u 0.262s 0:08.19 94.5% 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 Mon Oct 10 2011 at 19:33:22 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: 334 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3071 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 2.503203 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): -29.58200 34.41600 ymin,ymax (A): -21.59900 25.78700 zmin,zma (A): -7.154000 39.02300 x,y,z range (A): 63.99800 47.38600 46.17700 scale (grids/A): 2.503203 object centre (A): 2.417001 2.094000 15.93450 number of atom coordinates read : 3071 total number of charged atoms : 2930 net assigned charge : -0.4859794 assigned positive charge : 467.4518 centred at (gu) : 91.92345 90.61162 88.87554 assigned negative charge : -467.9389 centred at (gu) : 92.05956 89.88656 88.43592 start vw surface at 0.1500000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 155494 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27806 grid for indexing accessible points = 1.400000 m= 69167 mr = 109264 m= 19356 mr = 53640 m= 3218 mr = 14169 m= 268 mr = 2116 m= 6 mr = 132 m= 0 mr = 0 time to grow re-entrant surface = 0.6200000 no. cavity mid-points inaccessible to solvent = 119 time to turn everything in is 1.110000 number of dielectric boundary points 68188 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 1.250000 number of grid points assigned charge 23422 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) : 1.668802 object centre at (A) : 2.417001 2.094000 15.93450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.8784749E-02 7.4207015E-02 midg,1,midg; midg,igrid,midg -0.2431792 0.1685148 1,midg,midg; igrid,midg,midg -0.3143750 -0.3599451 gauss-seidel spectral radius is 0.9991686 estimated iterations to convergence 274 setup time was (sec) 1.420000 now iterating at: 19:33:24 rms-change max change #iterations 9.224337 339.7333 at 10iterations 5.202812 143.6593 at 20iterations 2.922914 70.31325 at 30iterations 1.635478 33.46169 at 40iterations 0.9163740 19.74757 at 50iterations 0.5116844 10.24418 at 60iterations 0.2849040 6.104605 at 70iterations 0.1586946 3.117458 at 80iterations 8.8128515E-02 1.932350 at 90iterations 4.9002253E-02 0.9265480 at 100iterations 2.7247656E-02 0.5352268 at 110iterations 1.5114694E-02 0.3061943 at 120iterations 8.3876308E-03 0.1676235 at 130iterations 4.6705329E-03 9.6071243E-02 at 140iterations 2.5907487E-03 5.6657791E-02 at 150iterations 1.4393659E-03 2.8345108E-02 at 160iterations 7.9945032E-04 1.5504837E-02 at 170iterations 4.4253710E-04 9.6940994E-03 at 180iterations finished qdiffx linear iterations at : 19:33:34 total time elapsed so far: 11.53000 # loops : 180 mean,max change (kT/e) : 4.4253710E-04 9.6940994E-03 energy calculations done at 11.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.70000 DelPhi exited at 19:33:35 11.703u 0.231s 0:12.59 94.7% 0+0k 0+0io 0pf+0w