Sun Oct 9 11:53:31 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 Sun Oct 9 2011 at 11:53:31 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 = 2687 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: 0.6772825 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): 51.10200 103.6650 ymin,ymax (A): 5.018000 55.91400 zmin,zma (A): 36.05300 88.58000 x,y,z range (A): 52.56300 50.89600 52.52700 scale (grids/A): 0.6772825 object centre (A): 77.38350 30.46600 62.31650 number of atom coordinates read : 2687 total number of charged atoms : 2546 net assigned charge : 0.5000091 assigned positive charge : 383.2423 centred at (gu) : 89.28359 89.94738 92.10482 assigned negative charge : -382.7438 centred at (gu) : 89.45792 90.03275 92.01158 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 8943 nv = 96 ne = 84 npr = 53147 no. pairs analyzed = 53147 no. exposed pairs = 3619 no. arc points = 25833 no. surface atoms = 1222 nbur = 1465 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 640 mr = 4752 m= 3 mr = 125 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.2000000 number of dielectric boundary points 4709 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2143 ## 119 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 9719 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7624687E-08 4.4431086E-08 midg,1,midg; midg,igrid,midg 2.6568790E-08 -2.4516687E-08 1,midg,midg; igrid,midg,midg 6.0562641E-08 -4.4930285E-08 gauss-seidel spectral radius is 0.9887289 estimated iterations to convergence 77 setup time was (sec) 0.3900000 now iterating at: 11:53:32 rms-change max change #iterations 0.1860342 26.61485 at 10iterations 2.1317285E-02 2.934610 at 20iterations 2.5829629E-03 0.3093910 at 30iterations 4.4215968E-04 6.5944672E-02 at 40iterations 1.2737991E-04 2.2083282E-02 at 50iterations finished qdiffx linear iterations at : 11:53:34 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 1.2737991E-04 2.2083282E-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) 3.380000 DelPhi exited at 11:53:35 3.388u 0.178s 0:03.84 92.4% 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 11:53:35 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 = 2687 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: 2.031847 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): 51.10200 103.6650 ymin,ymax (A): 5.018000 55.91400 zmin,zma (A): 36.05300 88.58000 x,y,z range (A): 52.56300 50.89600 52.52700 scale (grids/A): 2.031847 object centre (A): 77.38350 30.46600 62.31650 number of atom coordinates read : 2687 total number of charged atoms : 2546 net assigned charge : 0.5000091 assigned positive charge : 383.2423 centred at (gu) : 87.85027 89.84132 96.31375 assigned negative charge : -382.7438 centred at (gu) : 88.37373 90.09818 96.03462 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 93766 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25833 grid for indexing accessible points = 1.400000 m= 37396 mr = 63538 m= 8164 mr = 27425 m= 786 mr = 5533 m= 10 mr = 354 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 428 time to turn everything in is 0.4600000 number of dielectric boundary points 43273 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 77 iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 20189 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) : 0.6772825 object centre at (A) : 77.38350 30.46600 62.31650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6093189E-02 8.0650076E-02 midg,1,midg; midg,igrid,midg 1.9937016E-02 -1.2263209E-02 1,midg,midg; igrid,midg,midg 3.4470279E-02 -5.1686410E-02 gauss-seidel spectral radius is 0.9988284 estimated iterations to convergence 231 setup time was (sec) 0.6700000 now iterating at: 11:53:36 rms-change max change #iterations 4.787559 204.5322 at 10iterations 2.370677 71.63791 at 20iterations 1.166387 32.11787 at 30iterations 0.5795592 17.56967 at 40iterations 0.2881368 8.817886 at 50iterations 0.1424137 4.247084 at 60iterations 7.0704103E-02 1.924961 at 70iterations 3.5081655E-02 0.9471931 at 80iterations 1.7459938E-02 0.4686661 at 90iterations 8.6908387E-03 0.2456169 at 100iterations 4.3534874E-03 0.1153021 at 110iterations 2.2043737E-03 6.8202972E-02 at 120iterations finished qdiffx linear iterations at : 11:53:43 total time elapsed so far: 7.760000 # loops : 120 mean,max change (kT/e) : 2.2043737E-03 6.8202972E-02 energy calculations done at 7.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.890000 DelPhi exited at 11:53:43 7.890u 0.209s 0:08.40 96.3% 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 Sun Oct 9 2011 at 11:53:43 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 = 2687 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: 3.047771 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): 51.10200 103.6650 ymin,ymax (A): 5.018000 55.91400 zmin,zma (A): 36.05300 88.58000 x,y,z range (A): 52.56300 50.89600 52.52700 scale (grids/A): 3.047771 object centre (A): 77.38350 30.46600 62.31650 number of atom coordinates read : 2687 total number of charged atoms : 2546 net assigned charge : 0.5000091 assigned positive charge : 383.2423 centred at (gu) : 86.77512 89.76186 99.47061 assigned negative charge : -382.7438 centred at (gu) : 87.56042 90.14729 99.05190 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 216321 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25833 grid for indexing accessible points = 1.400000 m= 113173 mr = 154247 m= 49334 mr = 91671 m= 15750 mr = 39869 m= 3307 mr = 12267 m= 277 mr = 2425 m= 6 mr = 142 m= 0 mr = 0 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 1542 time to turn everything in is 1.230000 number of dielectric boundary points 97547 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 20368 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) : 2.031847 object centre at (A) : 77.38350 30.46600 62.31650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1073494 0.9439166 midg,1,midg; midg,igrid,midg 0.1900518 -0.3602757 1,midg,midg; igrid,midg,midg 0.2824588 -0.4600154 gauss-seidel spectral radius is 0.9993284 estimated iterations to convergence 304 setup time was (sec) 1.480000 now iterating at: 11:53:45 rms-change max change #iterations 11.08056 492.0340 at 10iterations 6.695242 157.0539 at 20iterations 4.039461 91.02049 at 30iterations 2.424945 47.15211 at 40iterations 1.451431 31.68596 at 50iterations 0.8670795 14.69022 at 60iterations 0.5155484 9.146698 at 70iterations 0.3063253 4.728451 at 80iterations 0.1817841 3.469769 at 90iterations 0.1079703 1.684601 at 100iterations 6.3834637E-02 1.030202 at 110iterations 3.7865002E-02 0.6224217 at 120iterations 2.2384176E-02 0.3669462 at 130iterations 1.3284525E-02 0.2173905 at 140iterations 7.8886198E-03 0.1423283 at 150iterations 4.7163041E-03 7.2135925E-02 at 160iterations 2.8371855E-03 5.2856445E-02 at 170iterations 1.7344241E-03 3.0734062E-02 at 180iterations finished qdiffx linear iterations at : 11:53:57 total time elapsed so far: 13.15000 # loops : 180 mean,max change (kT/e) : 1.7344241E-03 3.0734062E-02 energy calculations done at 13.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.28000 DelPhi exited at 11:53:57 13.278u 0.213s 0:13.76 97.9% 0+0k 0+0io 0pf+0w