Sat Oct 15 12:25:43 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 Sat Oct 15 2011 at 12:25:43 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1946 !!! WARNING: ASP 186 has a net charge of -2.0000 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: 0.6653459 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): 1.259000 44.13000 ymin,ymax (A): -9.286000 37.76000 zmin,zma (A): -24.70100 28.80500 x,y,z range (A): 42.87100 47.04600 53.50600 scale (grids/A): 0.6653459 object centre (A): 22.69450 14.23700 2.052000 number of atom coordinates read : 1946 total number of charged atoms : 1807 net assigned charge : 0.5000144 assigned positive charge : 287.9030 centred at (gu) : 90.05215 89.31112 88.27567 assigned negative charge : -287.4032 centred at (gu) : 89.85532 89.16482 88.18157 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5747 nv = 96 ne = 84 npr = 40435 no. pairs analyzed = 40435 no. exposed pairs = 2452 no. arc points = 17675 no. surface atoms = 825 nbur = 1121 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 385 mr = 3086 m= 2 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 51 time to turn everything in is 0.1700000 number of dielectric boundary points 2982 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1731 ## 145 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 6688 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.0102139E-08 1.2287588E-08 midg,1,midg; midg,igrid,midg -2.6440272E-08 2.2584610E-08 1,midg,midg; igrid,midg,midg -3.1245744E-08 3.4607329E-08 gauss-seidel spectral radius is 0.9882318 estimated iterations to convergence 75 setup time was (sec) 0.4000000 now iterating at: 12:25:43 rms-change max change #iterations 0.1442892 26.56521 at 10iterations 1.5246619E-02 2.370777 at 20iterations 1.6261527E-03 0.2679672 at 30iterations 1.7839752E-04 3.1864166E-02 at 40iterations 1.9082450E-05 3.3493042E-03 at 50iterations finished qdiffx linear iterations at : 12:25:47 total time elapsed so far: 3.790000 # loops : 50 mean,max change (kT/e) : 1.9082450E-05 3.3493042E-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 12:25:47 3.929u 0.245s 0:04.44 93.6% 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 Sat Oct 15 2011 at 12:25:47 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1946 !!! WARNING: ASP 186 has a net charge of -2.0000 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: 1.996038 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): 1.259000 44.13000 ymin,ymax (A): -9.286000 37.76000 zmin,zma (A): -24.70100 28.80500 x,y,z range (A): 42.87100 47.04600 53.50600 scale (grids/A): 1.996038 object centre (A): 22.69450 14.23700 2.052000 number of atom coordinates read : 1946 total number of charged atoms : 1807 net assigned charge : 0.5000144 assigned positive charge : 287.9030 centred at (gu) : 90.15643 87.93346 84.82691 assigned negative charge : -287.4032 centred at (gu) : 89.56622 87.49447 84.54475 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 60939 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17675 grid for indexing accessible points = 1.400000 m= 22799 mr = 41050 m= 4010 mr = 16919 m= 258 mr = 2623 m= 2 mr = 90 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 722 time to turn everything in is 0.3300000 number of dielectric boundary points 27326 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 101 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 14266 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) : 0.6653459 object centre at (A) : 22.69450 14.23700 2.052000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.0491553E-02 3.2240987E-02 midg,1,midg; midg,igrid,midg -1.9504687E-02 1.3500093E-02 1,midg,midg; igrid,midg,midg -2.7238401E-02 2.6585842E-02 gauss-seidel spectral radius is 0.9986871 estimated iterations to convergence 219 setup time was (sec) 0.5900000 now iterating at: 12:25:48 rms-change max change #iterations 3.953368 223.1115 at 10iterations 1.867765 71.18861 at 20iterations 0.8842488 33.03783 at 30iterations 0.4196559 14.70515 at 40iterations 0.1987326 6.754929 at 50iterations 9.4616614E-02 3.430766 at 60iterations 4.4884022E-02 1.555213 at 70iterations 2.1244014E-02 0.6917717 at 80iterations 1.0109799E-02 0.3397217 at 90iterations 4.7930465E-03 0.1795845 at 100iterations 2.2778215E-03 9.5674515E-02 at 110iterations 1.0816908E-03 3.7185669E-02 at 120iterations finished qdiffx linear iterations at : 12:25:56 total time elapsed so far: 8.860000 # loops : 120 mean,max change (kT/e) : 1.0816908E-03 3.7185669E-02 energy calculations done at 8.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.000000 DelPhi exited at 12:25:57 9.002u 0.276s 0:09.54 97.1% 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 Sat Oct 15 2011 at 12:25:57 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1946 !!! WARNING: ASP 186 has a net charge of -2.0000 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: 2.994057 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): 1.259000 44.13000 ymin,ymax (A): -9.286000 37.76000 zmin,zma (A): -24.70100 28.80500 x,y,z range (A): 42.87100 47.04600 53.50600 scale (grids/A): 2.994057 object centre (A): 22.69450 14.23700 2.052000 number of atom coordinates read : 1946 total number of charged atoms : 1807 net assigned charge : 0.5000144 assigned positive charge : 287.9030 centred at (gu) : 90.23476 86.90025 82.24049 assigned negative charge : -287.4032 centred at (gu) : 89.34927 86.24171 81.81714 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 140339 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17675 grid for indexing accessible points = 1.400000 m= 71437 mr = 99125 m= 27908 mr = 58381 m= 7366 mr = 22786 m= 1132 mr = 5672 m= 67 mr = 756 m= 4 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 2632 time to turn everything in is 0.8700000 number of dielectric boundary points 61498 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 14456 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) : 1.996038 object centre at (A) : 22.69450 14.23700 2.052000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5954407 0.9711316 midg,1,midg; midg,igrid,midg -0.1130574 0.1439183 1,midg,midg; igrid,midg,midg -0.2382023 0.2520878 gauss-seidel spectral radius is 0.9992596 estimated iterations to convergence 290 setup time was (sec) 1.170000 now iterating at: 12:25:58 rms-change max change #iterations 9.079705 401.1165 at 10iterations 5.240452 152.4412 at 20iterations 3.021373 72.02116 at 30iterations 1.737770 38.66955 at 40iterations 1.001196 19.16659 at 50iterations 0.5748839 11.38761 at 60iterations 0.3312596 6.868631 at 70iterations 0.1899968 4.014496 at 80iterations 0.1088945 2.272720 at 90iterations 6.2421460E-02 1.193174 at 100iterations 3.5880350E-02 0.6748557 at 110iterations 2.0541223E-02 0.4114666 at 120iterations 1.1794587E-02 0.2383494 at 130iterations 6.7551960E-03 0.1349144 at 140iterations 3.8745764E-03 7.2643280E-02 at 150iterations 2.2264074E-03 4.3069124E-02 at 160iterations 1.2783187E-03 2.6154995E-02 at 170iterations 7.3098962E-04 1.4151573E-02 at 180iterations finished qdiffx linear iterations at : 12:26:12 total time elapsed so far: 14.80000 # loops : 180 mean,max change (kT/e) : 7.3098962E-04 1.4151573E-02 energy calculations done at 14.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.94000 DelPhi exited at 12:26:12 14.939u 0.305s 0:15.52 98.1% 0+0k 0+0io 0pf+0w