Sun Oct 9 02:52:21 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 02:52:21 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2166 !!! WARNING: SEP 117 has a net charge of -0.4750 !!! WARNING: GLM 118 has a net charge of -0.0940 !!! WARNING: HIT 140 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6368401 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): -16.71700 23.66700 ymin,ymax (A): 0.8479999 44.04000 zmin,zma (A): -19.42800 36.47300 x,y,z range (A): 40.38400 43.19200 55.90100 scale (grids/A): 0.6368401 object centre (A): 3.475000 22.44400 8.522502 number of atom coordinates read : 2166 total number of charged atoms : 2028 net assigned charge : -4.554987 assigned positive charge : 325.2886 centred at (gu) : 90.49384 90.42883 90.62872 assigned negative charge : -329.8439 centred at (gu) : 90.46933 90.40473 90.63081 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5819 nv = 96 ne = 84 npr = 45754 no. pairs analyzed = 45754 no. exposed pairs = 2456 no. arc points = 17069 no. surface atoms = 843 nbur = 1323 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 318 mr = 3383 m= 1 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.1800000 number of dielectric boundary points 2706 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1648 ## 147 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 6927 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.1664455E-09 -7.1399784E-09 midg,1,midg; midg,igrid,midg -7.5556494E-09 -4.2382124E-09 1,midg,midg; igrid,midg,midg -7.4873867E-09 -4.2526676E-09 gauss-seidel spectral radius is 0.9871811 estimated iterations to convergence 72 setup time was (sec) 0.3700000 now iterating at: 02:52:22 rms-change max change #iterations 0.1332847 18.36847 at 10iterations 1.4091227E-02 2.186783 at 20iterations 2.4247395E-03 0.4514008 at 30iterations 7.0856517E-04 0.1467133 at 40iterations 2.3578556E-04 4.9270630E-02 at 50iterations finished qdiffx linear iterations at : 02:52:24 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 2.3578556E-04 4.9270630E-02 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 02:52:25 3.391u 0.169s 0:03.83 92.6% 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 Sun Oct 9 2011 at 02:52:25 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2166 !!! WARNING: SEP 117 has a net charge of -0.4750 !!! WARNING: GLM 118 has a net charge of -0.0940 !!! WARNING: HIT 140 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.910520 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): -16.71700 23.66700 ymin,ymax (A): 0.8479999 44.04000 zmin,zma (A): -19.42800 36.47300 x,y,z range (A): 40.38400 43.19200 55.90100 scale (grids/A): 1.910520 object centre (A): 3.475000 22.44400 8.522502 number of atom coordinates read : 2166 total number of charged atoms : 2028 net assigned charge : -4.554987 assigned positive charge : 325.2886 centred at (gu) : 91.48136 91.28623 91.88593 assigned negative charge : -329.8439 centred at (gu) : 91.40786 91.21423 91.89246 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 62910 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17069 grid for indexing accessible points = 1.400000 m= 22694 mr = 44802 m= 3623 mr = 17225 m= 221 mr = 2447 m= 4 mr = 94 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 572 time to turn everything in is 0.3100000 number of dielectric boundary points 24884 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 131 iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 15952 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) : 0.6368401 object centre at (A) : 3.475000 22.44400 8.522502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.9784729E-03 8.8119674E-03 midg,1,midg; midg,igrid,midg -4.4892826E-03 -1.1248415E-02 1,midg,midg; igrid,midg,midg -9.8576378E-03 -7.0985463E-03 gauss-seidel spectral radius is 0.9985887 estimated iterations to convergence 211 setup time was (sec) 0.5300000 now iterating at: 02:52:26 rms-change max change #iterations 3.914408 158.9856 at 10iterations 1.818126 61.06722 at 20iterations 0.8427886 29.57548 at 30iterations 0.3932992 13.80119 at 40iterations 0.1821825 6.364113 at 50iterations 8.5187666E-02 2.831541 at 60iterations 3.9782744E-02 1.495725 at 70iterations 1.8896909E-02 0.6167755 at 80iterations 9.2120748E-03 0.3653870 at 90iterations 4.7113737E-03 0.1913185 at 100iterations 2.5868248E-03 0.1097412 at 110iterations 1.5594951E-03 7.3959351E-02 at 120iterations finished qdiffx linear iterations at : 02:52:33 total time elapsed so far: 7.590000 # loops : 120 mean,max change (kT/e) : 1.5594951E-03 7.3959351E-02 energy calculations done at 7.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.730000 DelPhi exited at 02:52:33 7.736u 0.189s 0:08.20 96.4% 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 02:52:33 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2166 !!! WARNING: SEP 117 has a net charge of -0.4750 !!! WARNING: GLM 118 has a net charge of -0.0940 !!! WARNING: HIT 140 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.865781 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): -16.71700 23.66700 ymin,ymax (A): 0.8479999 44.04000 zmin,zma (A): -19.42800 36.47300 x,y,z range (A): 40.38400 43.19200 55.90100 scale (grids/A): 2.865781 object centre (A): 3.475000 22.44400 8.522502 number of atom coordinates read : 2166 total number of charged atoms : 2028 net assigned charge : -4.554987 assigned positive charge : 325.2886 centred at (gu) : 92.22198 91.92921 92.82877 assigned negative charge : -329.8439 centred at (gu) : 92.11175 91.82130 92.83863 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 145653 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17069 grid for indexing accessible points = 1.400000 m= 73959 mr = 108406 m= 26976 mr = 61505 m= 6658 mr = 22230 m= 1045 mr = 5318 m= 65 mr = 777 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 2083 time to turn everything in is 0.8000000 number of dielectric boundary points 56097 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 16223 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) : 1.910520 object centre at (A) : 3.475000 22.44400 8.522502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4432895 0.2290478 midg,1,midg; midg,igrid,midg -5.0645128E-02 -0.1291220 1,midg,midg; igrid,midg,midg -0.1321350 -5.1294196E-02 gauss-seidel spectral radius is 0.9992290 estimated iterations to convergence 284 setup time was (sec) 1.030000 now iterating at: 02:52:34 rms-change max change #iterations 9.079467 362.2007 at 10iterations 5.198309 129.8160 at 20iterations 2.974171 65.81705 at 30iterations 1.701119 38.26057 at 40iterations 0.9668584 20.14471 at 50iterations 0.5504045 11.28235 at 60iterations 0.3132321 6.142296 at 70iterations 0.1780992 3.723104 at 80iterations 0.1015477 2.070522 at 90iterations 5.7874657E-02 1.075484 at 100iterations 3.2928631E-02 0.6609297 at 110iterations 1.8755494E-02 0.3642330 at 120iterations 1.0754562E-02 0.2221947 at 130iterations 6.2360461E-03 0.1201019 at 140iterations 3.6628852E-03 7.3089600E-02 at 150iterations 2.2188283E-03 5.0163269E-02 at 160iterations 1.4102492E-03 3.2035828E-02 at 170iterations 9.5775729E-04 2.3681641E-02 at 180iterations finished qdiffx linear iterations at : 02:52:45 total time elapsed so far: 12.17000 # loops : 180 mean,max change (kT/e) : 9.5775729E-04 2.3681641E-02 energy calculations done at 12.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.30000 DelPhi exited at 02:52:46 12.298u 0.205s 0:12.77 97.8% 0+0k 0+0io 0pf+0w