Sun Oct 9 11:32:01 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 Sun Oct 9 2011 at 11:32:01 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2943 !!! WARNING: CME 112 has a net charge of -0.3480 !!! WARNING: HIR 211 has a net charge of 0.5140 !!! WARNING: CME 217 has a net charge of -0.3480 !!! WARNING: CME 314 has a net charge of -0.3480 !!! WARNING: CME 454 has a net charge of -0.3480 !!! WARNING: CME 2 has a net charge of 0.1000 !!! WARNING: CME 4 has a net charge of 0.1000 !!! WARNING: CME 6 has a net charge of 0.1000 !!! WARNING: CME 8 has a net charge of 0.1000 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: 0.5865102 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): -20.48000 40.21800 ymin,ymax (A): -25.55800 23.99700 zmin,zma (A): -27.88700 27.39400 x,y,z range (A): 60.69800 49.55500 55.28100 scale (grids/A): 0.5865102 object centre (A): 9.869001 -0.7805004 -0.2465000 number of atom coordinates read : 2943 total number of charged atoms : 2803 net assigned charge : 1.522030 assigned positive charge : 432.2690 centred at (gu) : 89.57339 90.89799 91.02275 assigned negative charge : -430.7487 centred at (gu) : 89.56753 90.83086 90.96558 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6982 nv = 96 ne = 84 npr = 58445 no. pairs analyzed = 58445 no. exposed pairs = 4094 no. arc points = 28450 no. surface atoms = 1346 nbur = 1597 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 = 1.484000 m= 378 mr = 3554 m= 2 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3796 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2818 ## 273 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8617 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.9000268E-10 2.3894347E-09 midg,1,midg; midg,igrid,midg -1.1325281E-09 2.6402411E-09 1,midg,midg; igrid,midg,midg 2.4871069E-10 4.8663612E-10 gauss-seidel spectral radius is 0.9850031 estimated iterations to convergence 67 setup time was (sec) 0.5500000 now iterating at: 11:32:02 rms-change max change #iterations 0.1015388 17.24936 at 10iterations 8.1861280E-03 1.303757 at 20iterations 8.9771987E-04 0.1402531 at 30iterations 1.8501595E-04 2.7235985E-02 at 40iterations 5.2233478E-05 7.9116821E-03 at 50iterations finished qdiffx linear iterations at : 11:32:05 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 5.2233478E-05 7.9116821E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 11:32:05 3.408u 0.215s 0:03.90 92.5% 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 Sun Oct 9 2011 at 11:32:05 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2943 !!! WARNING: CME 112 has a net charge of -0.3480 !!! WARNING: HIR 211 has a net charge of 0.5140 !!! WARNING: CME 217 has a net charge of -0.3480 !!! WARNING: CME 314 has a net charge of -0.3480 !!! WARNING: CME 454 has a net charge of -0.3480 !!! WARNING: CME 2 has a net charge of 0.1000 !!! WARNING: CME 4 has a net charge of 0.1000 !!! WARNING: CME 6 has a net charge of 0.1000 !!! WARNING: CME 8 has a net charge of 0.1000 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: 1.759531 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): -20.48000 40.21800 ymin,ymax (A): -25.55800 23.99700 zmin,zma (A): -27.88700 27.39400 x,y,z range (A): 60.69800 49.55500 55.28100 scale (grids/A): 1.759531 object centre (A): 9.869001 -0.7805004 -0.2465000 number of atom coordinates read : 2943 total number of charged atoms : 2803 net assigned charge : 1.522030 assigned positive charge : 432.2690 centred at (gu) : 88.71935 92.69289 93.06727 assigned negative charge : -430.7487 centred at (gu) : 88.70246 92.49261 92.89658 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 75557 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28450 grid for indexing accessible points = 1.400000 m= 26081 mr = 50574 m= 3732 mr = 17824 m= 193 mr = 1923 m= 3 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 35221 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 200 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 21835 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) : 0.5865102 object centre at (A) : 9.869001 -0.7805004 -0.2465000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2029859E-02 1.0187512E-02 midg,1,midg; midg,igrid,midg 5.7188557E-03 1.8452862E-02 1,midg,midg; igrid,midg,midg 1.2736938E-02 -1.0619042E-02 gauss-seidel spectral radius is 0.9984636 estimated iterations to convergence 202 setup time was (sec) 0.8600000 now iterating at: 11:32:06 rms-change max change #iterations 3.839488 160.2135 at 10iterations 1.707609 60.46113 at 20iterations 0.7651285 27.62017 at 30iterations 0.3405467 11.56620 at 40iterations 0.1523823 5.054417 at 50iterations 6.8121448E-02 2.400606 at 60iterations 3.0542513E-02 0.9729300 at 70iterations 1.3716238E-02 0.4509478 at 80iterations 6.2321657E-03 0.2083015 at 90iterations 2.8461018E-03 9.1211319E-02 at 100iterations 1.3326586E-03 4.7437668E-02 at 110iterations 6.4683013E-04 2.2312164E-02 at 120iterations finished qdiffx linear iterations at : 11:32:13 total time elapsed so far: 7.580000 # loops : 120 mean,max change (kT/e) : 6.4683013E-04 2.2312164E-02 energy calculations done at 7.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.760000 DelPhi exited at 11:32:13 7.767u 0.213s 0:08.27 96.3% 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 11:32:14 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2943 !!! WARNING: CME 112 has a net charge of -0.3480 !!! WARNING: HIR 211 has a net charge of 0.5140 !!! WARNING: CME 217 has a net charge of -0.3480 !!! WARNING: CME 314 has a net charge of -0.3480 !!! WARNING: CME 454 has a net charge of -0.3480 !!! WARNING: CME 2 has a net charge of 0.1000 !!! WARNING: CME 4 has a net charge of 0.1000 !!! WARNING: CME 6 has a net charge of 0.1000 !!! WARNING: CME 8 has a net charge of 0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.639296 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): -20.48000 40.21800 ymin,ymax (A): -25.55800 23.99700 zmin,zma (A): -27.88700 27.39400 x,y,z range (A): 60.69800 49.55500 55.28100 scale (grids/A): 2.639296 object centre (A): 9.869001 -0.7805004 -0.2465000 number of atom coordinates read : 2943 total number of charged atoms : 2803 net assigned charge : 1.522030 assigned positive charge : 432.2690 centred at (gu) : 88.07875 94.03930 94.60077 assigned negative charge : -430.7487 centred at (gu) : 88.05370 93.73888 94.34476 start vw surface at 0.1500000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 174791 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28450 grid for indexing accessible points = 1.400000 m= 85009 mr = 123802 m= 29525 mr = 66444 m= 6451 mr = 22283 m= 692 mr = 4209 m= 27 mr = 298 m= 2 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.330000 number of dielectric boundary points 79461 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.470000 number of grid points assigned charge 22414 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) : 1.759531 object centre at (A) : 9.869001 -0.7805004 -0.2465000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1741721 0.1334528 midg,1,midg; midg,igrid,midg 0.1308448 0.1757227 1,midg,midg; igrid,midg,midg 0.2740223 -0.1315696 gauss-seidel spectral radius is 0.9992262 estimated iterations to convergence 284 setup time was (sec) 1.650000 now iterating at: 11:32:15 rms-change max change #iterations 9.586445 294.2649 at 10iterations 5.609373 146.2687 at 20iterations 3.248881 78.25458 at 30iterations 1.876811 41.63866 at 40iterations 1.078065 21.91501 at 50iterations 0.6191992 14.07119 at 60iterations 0.3545459 6.917728 at 70iterations 0.2024239 3.955608 at 80iterations 0.1157000 2.205087 at 90iterations 6.5805830E-02 1.310173 at 100iterations 3.7482221E-02 0.7489204 at 110iterations 2.1330211E-02 0.4260902 at 120iterations 1.2172967E-02 0.2577515 at 130iterations 6.9490848E-03 0.1257935 at 140iterations 3.9726351E-03 7.7640533E-02 at 150iterations 2.2891210E-03 4.7387123E-02 at 160iterations 1.3272790E-03 2.6224136E-02 at 170iterations 7.8594184E-04 2.2143364E-02 at 180iterations finished qdiffx linear iterations at : 11:32:26 total time elapsed so far: 12.51000 # loops : 180 mean,max change (kT/e) : 7.8594184E-04 2.2143364E-02 energy calculations done at 12.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.68000 DelPhi exited at 11:32:27 12.685u 0.227s 0:13.19 97.8% 0+0k 0+0io 0pf+0w