Sun Oct 9 06:43:41 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 06:43:41 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1995 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 has a net charge of -3.0000 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: 0.6655201 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): -24.25800 25.69300 ymin,ymax (A): 1.938000 46.14900 zmin,zma (A): -23.50500 29.98700 x,y,z range (A): 49.95100 44.21100 53.49200 scale (grids/A): 0.6655201 object centre (A): 0.7174988 24.04350 3.240999 number of atom coordinates read : 1995 total number of charged atoms : 1856 net assigned charge : -1.499990 assigned positive charge : 301.1900 centred at (gu) : 89.22979 89.13528 88.44470 assigned negative charge : -302.6901 centred at (gu) : 89.16323 89.37024 88.41749 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5905 nv = 96 ne = 84 npr = 42148 no. pairs analyzed = 42148 no. exposed pairs = 2446 no. arc points = 17566 no. surface atoms = 832 nbur = 1163 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 327 mr = 3259 m= 2 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.2400000 number of dielectric boundary points 2939 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1691 ## 135 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 6941 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2965474E-08 1.1348350E-10 midg,1,midg; midg,igrid,midg 4.3276074E-08 -3.9383579E-08 1,midg,midg; igrid,midg,midg -1.9285752E-08 6.0321446E-09 gauss-seidel spectral radius is 0.9882398 estimated iterations to convergence 75 setup time was (sec) 0.4600000 now iterating at: 06:43:42 rms-change max change #iterations 0.1555140 21.36759 at 10iterations 1.6798317E-02 2.907722 at 20iterations 1.8063196E-03 0.2628746 at 30iterations 1.9693623E-04 2.8785706E-02 at 40iterations 2.1111318E-05 3.1375885E-03 at 50iterations finished qdiffx linear iterations at : 06:43:44 total time elapsed so far: 2.860000 # loops : 50 mean,max change (kT/e) : 2.1111318E-05 3.1375885E-03 energy calculations done at 2.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.030000 DelPhi exited at 06:43:45 3.035u 0.139s 0:03.51 90.0% 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 Sun Oct 9 2011 at 06:43:45 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1995 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 has a net charge of -3.0000 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: 1.996560 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): -24.25800 25.69300 ymin,ymax (A): 1.938000 46.14900 zmin,zma (A): -23.50500 29.98700 x,y,z range (A): 49.95100 44.21100 53.49200 scale (grids/A): 1.996560 object centre (A): 0.7174988 24.04350 3.240999 number of atom coordinates read : 1995 total number of charged atoms : 1856 net assigned charge : -1.499990 assigned positive charge : 301.1900 centred at (gu) : 87.68939 87.40594 85.33400 assigned negative charge : -302.6901 centred at (gu) : 87.48981 88.11073 85.25270 start vw surface at 0.1400000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 63572 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17566 grid for indexing accessible points = 1.400000 m= 22426 mr = 43819 m= 3542 mr = 16604 m= 231 mr = 2214 m= 4 mr = 78 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 741 time to turn everything in is 0.4600000 number of dielectric boundary points 27060 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 85 iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 14688 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) : 0.6655201 object centre at (A) : 0.7174988 24.04350 3.240999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.1758133E-02 2.1331191E-02 midg,1,midg; midg,igrid,midg 6.1364986E-02 -3.2424975E-02 1,midg,midg; igrid,midg,midg -4.0354010E-02 -3.0488637E-03 gauss-seidel spectral radius is 0.9986889 estimated iterations to convergence 219 setup time was (sec) 0.7200000 now iterating at: 06:43:45 rms-change max change #iterations 4.105030 204.4505 at 10iterations 1.946437 84.76366 at 20iterations 0.9235377 32.03447 at 30iterations 0.4409053 17.79911 at 40iterations 0.2087980 6.724549 at 50iterations 9.9085934E-02 3.549286 at 60iterations 4.7002356E-02 1.549225 at 70iterations 2.2439051E-02 0.8486032 at 80iterations 1.0624538E-02 0.3626804 at 90iterations 5.0531384E-03 0.1635513 at 100iterations 2.4094726E-03 8.7371826E-02 at 110iterations 1.1474495E-03 3.6247253E-02 at 120iterations finished qdiffx linear iterations at : 06:43:51 total time elapsed so far: 6.570000 # loops : 120 mean,max change (kT/e) : 1.1474495E-03 3.6247253E-02 energy calculations done at 6.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.750000 DelPhi exited at 06:43:52 6.748u 0.153s 0:07.17 96.0% 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 Sun Oct 9 2011 at 06:43:52 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1995 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 has a net charge of -3.0000 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: 2.994840 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): -24.25800 25.69300 ymin,ymax (A): 1.938000 46.14900 zmin,zma (A): -23.50500 29.98700 x,y,z range (A): 49.95100 44.21100 53.49200 scale (grids/A): 2.994840 object centre (A): 0.7174988 24.04350 3.240999 number of atom coordinates read : 1995 total number of charged atoms : 1856 net assigned charge : -1.499990 assigned positive charge : 301.1900 centred at (gu) : 86.53411 86.10886 83.00101 assigned negative charge : -302.6901 centred at (gu) : 86.23478 87.16605 82.87906 start vw surface at 0.1400000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 147098 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17566 grid for indexing accessible points = 1.400000 m= 73213 mr = 106350 m= 25972 mr = 59983 m= 6394 mr = 20953 m= 1002 mr = 4808 m= 68 mr = 649 m= 4 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.6300000 no. cavity mid-points inaccessible to solvent = 2712 time to turn everything in is 1.140000 number of dielectric boundary points 60968 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 14848 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) : 1.996560 object centre at (A) : 0.7174988 24.04350 3.240999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.8145116 0.7013645 midg,1,midg; midg,igrid,midg 0.6924247 -0.3299801 1,midg,midg; igrid,midg,midg -0.3760931 3.3763912E-02 gauss-seidel spectral radius is 0.9992617 estimated iterations to convergence 290 setup time was (sec) 1.410000 now iterating at: 06:43:53 rms-change max change #iterations 9.402610 437.2861 at 10iterations 5.417907 126.4999 at 20iterations 3.119408 68.22217 at 30iterations 1.792497 33.80511 at 40iterations 1.033996 21.15186 at 50iterations 0.5937825 13.54152 at 60iterations 0.3402920 6.713615 at 70iterations 0.1952571 3.731976 at 80iterations 0.1120674 2.145293 at 90iterations 6.4378984E-02 1.201195 at 100iterations 3.6875900E-02 0.7391090 at 110iterations 2.1186233E-02 0.4156175 at 120iterations 1.2192950E-02 0.2361794 at 130iterations 6.9985222E-03 0.1352959 at 140iterations 4.0120832E-03 8.1990242E-02 at 150iterations 2.3108162E-03 4.4437408E-02 at 160iterations 1.3279320E-03 2.3883820E-02 at 170iterations 7.6861627E-04 1.4365673E-02 at 180iterations finished qdiffx linear iterations at : 06:44:03 total time elapsed so far: 10.97000 # loops : 180 mean,max change (kT/e) : 7.6861627E-04 1.4365673E-02 energy calculations done at 10.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.14000 DelPhi exited at 06:44:03 11.139u 0.172s 0:11.64 97.0% 0+0k 0+0io 0pf+0w