Tue Oct 11 03:46:38 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+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 Tue Oct 11 2011 at 03:46:39 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2776 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6453484 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): -9.351000 37.19600 ymin,ymax (A): -27.47500 21.98800 zmin,zma (A): -9.925000 45.23900 x,y,z range (A): 46.54700 49.46300 55.16400 scale (grids/A): 0.6453484 object centre (A): 13.92250 -2.743501 17.65700 number of atom coordinates read : 2776 total number of charged atoms : 2680 net assigned charge : 2.162019 assigned positive charge : 427.5785 centred at (gu) : 89.22417 90.67232 91.79799 assigned negative charge : -425.4172 centred at (gu) : 88.96262 90.56818 91.79125 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7753 nv = 96 ne = 84 npr = 54841 no. pairs analyzed = 54841 no. exposed pairs = 3492 no. arc points = 23999 no. surface atoms = 1178 nbur = 1598 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 425 mr = 4315 m= 3 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 32 time to turn everything in is 0.3600000 number of dielectric boundary points 3812 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2349 ## 214 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9359 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0404003E-09 7.1542217E-09 midg,1,midg; midg,igrid,midg -9.9834701E-09 2.2019391E-08 1,midg,midg; igrid,midg,midg -4.2266670E-08 3.4974118E-08 gauss-seidel spectral radius is 0.9875727 estimated iterations to convergence 73 setup time was (sec) 0.6200000 now iterating at: 03:46:39 rms-change max change #iterations 0.1599152 23.26239 at 10iterations 1.6195213E-02 2.515486 at 20iterations 1.6630080E-03 0.2058144 at 30iterations 1.6918592E-04 2.2262573E-02 at 40iterations 1.7770981E-05 2.4805069E-03 at 50iterations finished qdiffx linear iterations at : 03:46:43 total time elapsed so far: 3.940000 # loops : 50 mean,max change (kT/e) : 1.7770981E-05 2.4805069E-03 energy calculations done at 3.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.120000 DelPhi exited at 03:46:43 4.126u 0.288s 0:04.91 89.6% 0+0k 0+0io 6pf+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 Oct 11 2011 at 03:46:43 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2776 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 1.936045 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): -9.351000 37.19600 ymin,ymax (A): -27.47500 21.98800 zmin,zma (A): -9.925000 45.23900 x,y,z range (A): 46.54700 49.46300 55.16400 scale (grids/A): 1.936045 object centre (A): 13.92250 -2.743501 17.65700 number of atom coordinates read : 2776 total number of charged atoms : 2680 net assigned charge : 2.162019 assigned positive charge : 427.5785 centred at (gu) : 87.67180 92.01649 95.39320 assigned negative charge : -425.4172 centred at (gu) : 86.88750 91.70447 95.37351 start vw surface at 0.1600000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 83347 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23999 grid for indexing accessible points = 1.400000 m= 30772 mr = 58369 m= 4860 mr = 22733 m= 354 mr = 2888 m= 5 mr = 128 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 1607 time to turn everything in is 0.7400000 number of dielectric boundary points 35220 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 145 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 21105 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) : 0.6453484 object centre at (A) : 13.92250 -2.743501 17.65700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5140250E-02 1.1607011E-02 midg,1,midg; midg,igrid,midg -1.0928650E-02 7.9626497E-03 1,midg,midg; igrid,midg,midg -1.8074883E-02 4.9477294E-02 gauss-seidel spectral radius is 0.9986971 estimated iterations to convergence 219 setup time was (sec) 1.040000 now iterating at: 03:46:45 rms-change max change #iterations 4.602999 196.9719 at 10iterations 2.196874 81.14255 at 20iterations 1.047913 32.18567 at 30iterations 0.4996772 14.87142 at 40iterations 0.2381115 7.503810 at 50iterations 0.1131968 3.525894 at 60iterations 5.4337293E-02 1.667803 at 70iterations 2.5875447E-02 0.8100579 at 80iterations 1.2321056E-02 0.3973923 at 90iterations 5.8667976E-03 0.1731929 at 100iterations 2.8064724E-03 7.8876972E-02 at 110iterations 1.3392285E-03 3.9310455E-02 at 120iterations finished qdiffx linear iterations at : 03:46:53 total time elapsed so far: 9.590000 # loops : 120 mean,max change (kT/e) : 1.3392285E-03 3.9310455E-02 energy calculations done at 9.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.770000 DelPhi exited at 03:46:54 9.773u 0.321s 0:10.39 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 Tue Oct 11 2011 at 03:46:54 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2776 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 2.904068 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): -9.351000 37.19600 ymin,ymax (A): -27.47500 21.98800 zmin,zma (A): -9.925000 45.23900 x,y,z range (A): 46.54700 49.46300 55.16400 scale (grids/A): 2.904068 object centre (A): 13.92250 -2.743501 17.65700 number of atom coordinates read : 2776 total number of charged atoms : 2680 net assigned charge : 2.162019 assigned positive charge : 427.5785 centred at (gu) : 86.50756 93.02453 98.08971 assigned negative charge : -425.4172 centred at (gu) : 85.33112 92.55650 98.06010 start vw surface at 0.1500000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 192593 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23999 grid for indexing accessible points = 1.400000 m= 99708 mr = 141350 m= 36020 mr = 81767 m= 8664 mr = 28724 m= 1320 mr = 6257 m= 102 mr = 873 m= 0 mr = 49 time to grow re-entrant surface = 1.180000 no. cavity mid-points inaccessible to solvent = 5237 time to turn everything in is 1.920000 number of dielectric boundary points 79387 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 2.080000 number of grid points assigned charge 21430 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) : 1.936045 object centre at (A) : 13.92250 -2.743501 17.65700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2781758 0.4106989 midg,1,midg; midg,igrid,midg -0.1637342 3.6798250E-02 1,midg,midg; igrid,midg,midg -9.1063417E-02 0.4772063 gauss-seidel spectral radius is 0.9992810 estimated iterations to convergence 294 setup time was (sec) 2.250000 now iterating at: 03:46:57 rms-change max change #iterations 10.77952 426.0333 at 10iterations 6.366354 163.9300 at 20iterations 3.751795 99.20658 at 30iterations 2.199402 46.00073 at 40iterations 1.290141 25.99905 at 50iterations 0.7519122 14.99180 at 60iterations 0.4375641 7.576885 at 70iterations 0.2550393 4.381104 at 80iterations 0.1482702 3.121023 at 90iterations 8.6282283E-02 1.657468 at 100iterations 5.0023220E-02 0.8095474 at 110iterations 2.9132668E-02 0.4754210 at 120iterations 1.6900338E-02 0.3030453 at 130iterations 9.7987270E-03 0.1843176 at 140iterations 5.6864298E-03 9.6401215E-02 at 150iterations 3.3011921E-03 5.8976173E-02 at 160iterations 1.9142851E-03 3.4400940E-02 at 170iterations 1.1169441E-03 1.8053055E-02 at 180iterations finished qdiffx linear iterations at : 03:47:11 total time elapsed so far: 16.53000 # loops : 180 mean,max change (kT/e) : 1.1169441E-03 1.8053055E-02 energy calculations done at 16.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.71000 DelPhi exited at 03:47:12 16.716u 0.336s 0:17.65 96.5% 0+0k 0+0io 0pf+0w