Sat Oct 15 14:29:38 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 Sat Oct 15 2011 at 14:29:41 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2809 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: GLN 355 has a net charge of -0.2720 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: 0.6224756 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): -9.219000 47.97200 ymin,ymax (A): 4.144000 54.53200 zmin,zma (A): 7.406000 63.17000 x,y,z range (A): 57.19100 50.38800 55.76400 scale (grids/A): 0.6224756 object centre (A): 19.37650 29.33800 35.28800 number of atom coordinates read : 2809 total number of charged atoms : 2668 net assigned charge : -1.257969 assigned positive charge : 425.1432 centred at (gu) : 88.89345 89.35027 90.83511 assigned negative charge : -426.4023 centred at (gu) : 88.76279 89.51685 90.87337 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7401 nv = 96 ne = 84 npr = 55583 no. pairs analyzed = 55583 no. exposed pairs = 3757 no. arc points = 26760 no. surface atoms = 1268 nbur = 1541 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 377 mr = 3787 m= 1 mr = 33 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 3959 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2648 ## 243 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8931 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6288770E-09 -4.8354880E-09 midg,1,midg; midg,igrid,midg 1.3647858E-08 -1.2372137E-08 1,midg,midg; igrid,midg,midg -1.4596945E-08 7.0813284E-09 gauss-seidel spectral radius is 0.9866611 estimated iterations to convergence 71 setup time was (sec) 0.5900000 now iterating at: 14:29:43 rms-change max change #iterations 0.1331996 23.50888 at 10iterations 1.2315216E-02 1.580897 at 20iterations 1.1293924E-03 0.1423111 at 30iterations 1.0681372E-04 1.6674042E-02 at 40iterations 1.1305281E-05 2.2697449E-03 at 50iterations finished qdiffx linear iterations at : 14:29:53 total time elapsed so far: 4.040000 # loops : 50 mean,max change (kT/e) : 1.1305281E-05 2.2697449E-03 energy calculations done at 4.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.220000 DelPhi exited at 14:29:55 4.228u 0.262s 0:14.85 30.1% 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 14:29:56 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2809 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: GLN 355 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.867427 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): -9.219000 47.97200 ymin,ymax (A): 4.144000 54.53200 zmin,zma (A): 7.406000 63.17000 x,y,z range (A): 57.19100 50.38800 55.76400 scale (grids/A): 1.867427 object centre (A): 19.37650 29.33800 35.28800 number of atom coordinates read : 2809 total number of charged atoms : 2668 net assigned charge : -1.257969 assigned positive charge : 425.1432 centred at (gu) : 86.67949 88.04959 92.50418 assigned negative charge : -426.4023 centred at (gu) : 86.28796 88.55022 92.61961 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 79406 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26760 grid for indexing accessible points = 1.400000 m= 26713 mr = 52787 m= 3860 mr = 18678 m= 208 mr = 2181 m= 2 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 695 time to turn everything in is 0.5900000 number of dielectric boundary points 36479 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 199 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 20913 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) : 0.6224756 object centre at (A) : 19.37650 29.33800 35.28800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1536564E-03 7.1050046E-04 midg,1,midg; midg,igrid,midg 1.6625047E-02 -3.0949932E-02 1,midg,midg; igrid,midg,midg -5.2882951E-02 3.8751177E-02 gauss-seidel spectral radius is 0.9986157 estimated iterations to convergence 213 setup time was (sec) 0.9300000 now iterating at: 14:29:59 rms-change max change #iterations 4.319825 174.7862 at 10iterations 2.003053 70.96962 at 20iterations 0.9297990 27.78702 at 30iterations 0.4294704 13.71743 at 40iterations 0.2011091 6.420589 at 50iterations 9.3407549E-02 3.013691 at 60iterations 4.3283526E-02 1.508366 at 70iterations 2.0215362E-02 0.6028461 at 80iterations 9.3765333E-03 0.2830629 at 90iterations 4.3604602E-03 0.1299438 at 100iterations 2.0279801E-03 6.3225299E-02 at 110iterations 9.4835076E-04 2.9138565E-02 at 120iterations finished qdiffx linear iterations at : 14:30:18 total time elapsed so far: 9.830000 # loops : 120 mean,max change (kT/e) : 9.4835076E-04 2.9138565E-02 energy calculations done at 9.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.02000 DelPhi exited at 14:30:19 10.026u 0.293s 0:22.73 45.3% 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 Sat Oct 15 2011 at 14:30:23 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2809 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: GLN 355 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.801140 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): -9.219000 47.97200 ymin,ymax (A): 4.144000 54.53200 zmin,zma (A): 7.406000 63.17000 x,y,z range (A): 57.19100 50.38800 55.76400 scale (grids/A): 2.801140 object centre (A): 19.37650 29.33800 35.28800 number of atom coordinates read : 2809 total number of charged atoms : 2668 net assigned charge : -1.257969 assigned positive charge : 425.1432 centred at (gu) : 85.01918 87.07442 93.75606 assigned negative charge : -426.4023 centred at (gu) : 84.43189 87.82533 93.92937 start vw surface at 0.1400000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 183675 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26760 grid for indexing accessible points = 1.400000 m= 87645 mr = 128971 m= 29731 mr = 69280 m= 6464 mr = 22796 m= 784 mr = 4535 m= 39 mr = 496 m= 0 mr = 15 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 2027 time to turn everything in is 1.510000 number of dielectric boundary points 82245 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.670000 number of grid points assigned charge 21343 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) : 1.867427 object centre at (A) : 19.37650 29.33800 35.28800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2838458 0.1430279 midg,1,midg; midg,igrid,midg 0.1301599 -0.3248318 1,midg,midg; igrid,midg,midg -0.5529894 0.5089508 gauss-seidel spectral radius is 0.9992753 estimated iterations to convergence 293 setup time was (sec) 1.880000 now iterating at: 14:30:29 rms-change max change #iterations 10.43093 340.1343 at 10iterations 6.227563 187.7740 at 20iterations 3.668977 75.14156 at 30iterations 2.151082 42.77560 at 40iterations 1.259300 24.23872 at 50iterations 0.7335294 15.57568 at 60iterations 0.4261881 9.924481 at 70iterations 0.2470201 4.779234 at 80iterations 0.1434232 2.678875 at 90iterations 8.3060823E-02 1.483494 at 100iterations 4.8121218E-02 0.9496484 at 110iterations 2.7839145E-02 0.5268404 at 120iterations 1.6097704E-02 0.2954922 at 130iterations 9.3040485E-03 0.1637688 at 140iterations 5.3670150E-03 0.1077309 at 150iterations 3.1062493E-03 5.7748795E-02 at 160iterations 1.7943169E-03 3.3375740E-02 at 170iterations 1.0355423E-03 1.8936157E-02 at 180iterations finished qdiffx linear iterations at : 14:31:00 total time elapsed so far: 16.22000 # loops : 180 mean,max change (kT/e) : 1.0355423E-03 1.8936157E-02 energy calculations done at 16.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.40000 DelPhi exited at 14:31:02 16.405u 0.313s 0:39.67 42.1% 0+0k 0+0io 0pf+0w