Tue Nov 22 14:11:53 PST 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 Tue Nov 22 2011 at 14:11:59 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 0.6473198 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): -5.275000 34.66400 ymin,ymax (A): -3.524000 48.07100 zmin,zma (A): -24.21700 30.77900 x,y,z range (A): 39.93900 51.59500 54.99600 scale (grids/A): 0.6473198 object centre (A): 14.69450 22.27350 3.281001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.4260 centred at (gu) : 90.62794 92.68539 90.22141 assigned negative charge : -288.4263 centred at (gu) : 90.73696 92.80909 90.15769 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5598 nv = 96 ne = 84 npr = 40758 no. pairs analyzed = 40758 no. exposed pairs = 2486 no. arc points = 17565 no. surface atoms = 842 nbur = 1122 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 301 mr = 3093 m= 1 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 2767 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1803 ## 201 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 6645 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.4878499E-10 1.3016712E-08 midg,1,midg; midg,igrid,midg 1.0592244E-08 -1.3504537E-08 1,midg,midg; igrid,midg,midg 1.4950208E-08 -6.6147838E-09 gauss-seidel spectral radius is 0.9875765 estimated iterations to convergence 73 setup time was (sec) 0.3800000 now iterating at: 14:12:02 rms-change max change #iterations 0.1304122 19.21575 at 10iterations 1.3378901E-02 2.007468 at 20iterations 1.3572244E-03 0.2265379 at 30iterations 1.3601899E-04 1.8986285E-02 at 40iterations 1.3853465E-05 2.3651123E-03 at 50iterations finished qdiffx linear iterations at : 14:12:11 total time elapsed so far: 3.790000 # loops : 50 mean,max change (kT/e) : 1.3853465E-05 2.3651123E-03 energy calculations done at 3.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.930000 DelPhi exited at 14:12:12 3.931u 0.194s 0:13.63 30.2% 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 Tue Nov 22 2011 at 14:12:13 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 1.941959 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): -5.275000 34.66400 ymin,ymax (A): -3.524000 48.07100 zmin,zma (A): -24.21700 30.77900 x,y,z range (A): 39.93900 51.59500 54.99600 scale (grids/A): 1.941959 object centre (A): 14.69450 22.27350 3.281001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.4260 centred at (gu) : 91.88392 98.05598 90.66409 assigned negative charge : -288.4263 centred at (gu) : 92.21100 98.42757 90.47339 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 59640 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17565 grid for indexing accessible points = 1.400000 m= 21541 mr = 40774 m= 3292 mr = 16215 m= 130 mr = 2078 m= 1 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 602 time to turn everything in is 0.3200000 number of dielectric boundary points 25496 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 134 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 14470 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) : 0.6473198 object centre at (A) : 14.69450 22.27350 3.281001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6392057E-02 1.2916620E-02 midg,1,midg; midg,igrid,midg 3.1697404E-02 -9.8388363E-03 1,midg,midg; igrid,midg,midg 7.7915946E-03 -5.1650638E-03 gauss-seidel spectral radius is 0.9986071 estimated iterations to convergence 212 setup time was (sec) 0.5800000 now iterating at: 14:12:15 rms-change max change #iterations 3.762609 197.6628 at 10iterations 1.742229 66.80623 at 20iterations 0.8119931 31.39961 at 30iterations 0.3782311 12.46381 at 40iterations 0.1748150 6.820633 at 50iterations 8.1107482E-02 2.860622 at 60iterations 3.7663117E-02 1.355189 at 70iterations 1.7487861E-02 0.5939312 at 80iterations 8.1616435E-03 0.2975807 at 90iterations 3.7712739E-03 0.1344604 at 100iterations 1.7583917E-03 6.1943769E-02 at 110iterations 8.1537495E-04 3.0563354E-02 at 120iterations finished qdiffx linear iterations at : 14:12:40 total time elapsed so far: 8.990000 # loops : 120 mean,max change (kT/e) : 8.1537495E-04 3.0563354E-02 energy calculations done at 8.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.120000 DelPhi exited at 14:12:42 9.126u 0.370s 0:28.72 33.0% 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 Tue Nov 22 2011 at 14:12:44 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 2.912939 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): -5.275000 34.66400 ymin,ymax (A): -3.524000 48.07100 zmin,zma (A): -24.21700 30.77900 x,y,z range (A): 39.93900 51.59500 54.99600 scale (grids/A): 2.912939 object centre (A): 14.69450 22.27350 3.281001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.4260 centred at (gu) : 92.82581 102.0839 90.99605 assigned negative charge : -288.4263 centred at (gu) : 93.31661 102.6414 90.71014 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 137623 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17565 grid for indexing accessible points = 1.400000 m= 69090 mr = 98427 m= 25806 mr = 56901 m= 5813 mr = 21350 m= 645 mr = 4377 m= 40 mr = 421 m= 0 mr = 16 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 2102 time to turn everything in is 0.8400000 number of dielectric boundary points 57525 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 14656 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) : 1.941959 object centre at (A) : 14.69450 22.27350 3.281001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.058349 -1.0005571E-03 midg,1,midg; midg,igrid,midg 0.3240346 -0.1235263 1,midg,midg; igrid,midg,midg 4.5636680E-02 -3.8422544E-02 gauss-seidel spectral radius is 0.9992396 estimated iterations to convergence 286 setup time was (sec) 1.130000 now iterating at: 14:12:51 rms-change max change #iterations 8.800168 467.0774 at 10iterations 5.070041 164.9776 at 20iterations 2.904263 82.61128 at 30iterations 1.657494 38.90587 at 40iterations 0.9488629 18.86004 at 50iterations 0.5402779 12.30400 at 60iterations 0.3087294 6.203617 at 70iterations 0.1755861 3.674738 at 80iterations 9.9980623E-02 2.016934 at 90iterations 5.6809917E-02 1.173513 at 100iterations 3.2365471E-02 0.6029892 at 110iterations 1.8424841E-02 0.4062705 at 120iterations 1.0466937E-02 0.2138720 at 130iterations 5.9638191E-03 0.1190677 at 140iterations 3.4038436E-03 6.9265366E-02 at 150iterations 1.9327533E-03 3.8400650E-02 at 160iterations 1.0996161E-03 2.3711205E-02 at 170iterations 6.2593218E-04 1.2434959E-02 at 180iterations finished qdiffx linear iterations at : 14:13:33 total time elapsed so far: 15.04000 # loops : 180 mean,max change (kT/e) : 6.2593218E-04 1.2434959E-02 energy calculations done at 15.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.17000 DelPhi exited at 14:13:35 15.172u 0.298s 0:51.58 29.9% 0+0k 0+0io 0pf+0w