Sun Oct 9 00:40:36 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 00:40:36 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2271 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6519191 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): -0.5390000 54.06900 ymin,ymax (A): -14.51700 27.56900 zmin,zma (A): 30.69700 83.97600 x,y,z range (A): 54.60800 42.08600 53.27900 scale (grids/A): 0.6519191 object centre (A): 26.76500 6.526000 57.33650 number of atom coordinates read : 2271 total number of charged atoms : 2137 net assigned charge : 11.50002 assigned positive charge : 332.4886 centred at (gu) : 90.39805 88.56353 88.93838 assigned negative charge : -320.9893 centred at (gu) : 90.42352 88.65587 88.93204 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6587 nv = 96 ne = 84 npr = 45595 no. pairs analyzed = 45595 no. exposed pairs = 2986 no. arc points = 21245 no. surface atoms = 994 nbur = 1277 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 375 mr = 3456 m= 3 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3469 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2085 ## 199 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7770 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7743873E-08 1.9389306E-08 midg,1,midg; midg,igrid,midg 4.7619100E-08 8.2843163E-09 1,midg,midg; igrid,midg,midg 2.4480308E-08 2.1460927E-08 gauss-seidel spectral radius is 0.9877833 estimated iterations to convergence 74 setup time was (sec) 0.5000000 now iterating at: 00:40:36 rms-change max change #iterations 0.1430871 22.30103 at 10iterations 1.4649784E-02 2.075333 at 20iterations 1.5127240E-03 0.2162461 at 30iterations 1.6246212E-04 2.5505066E-02 at 40iterations 1.8539489E-05 2.7313232E-03 at 50iterations finished qdiffx linear iterations at : 00:40:39 total time elapsed so far: 2.890000 # loops : 50 mean,max change (kT/e) : 1.8539489E-05 2.7313232E-03 energy calculations done at 2.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.060000 DelPhi exited at 00:40:39 3.067u 0.143s 0:03.53 90.6% 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 00:40:39 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2271 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: 1.955757 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): -0.5390000 54.06900 ymin,ymax (A): -14.51700 27.56900 zmin,zma (A): 30.69700 83.97600 x,y,z range (A): 54.60800 42.08600 53.27900 scale (grids/A): 1.955757 object centre (A): 26.76500 6.526000 57.33650 number of atom coordinates read : 2271 total number of charged atoms : 2137 net assigned charge : 11.50002 assigned positive charge : 332.4886 centred at (gu) : 91.19405 85.69029 86.81489 assigned negative charge : -320.9893 centred at (gu) : 91.27077 85.96755 86.79642 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 70806 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21245 grid for indexing accessible points = 1.400000 m= 25369 mr = 47753 m= 4205 mr = 18278 m= 292 mr = 2483 m= 4 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 32074 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 134 iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 16884 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) : 0.6519191 object centre at (A) : 26.76500 6.526000 57.33650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6371427E-02 4.8246849E-02 midg,1,midg; midg,igrid,midg 4.2742357E-02 -3.0610408E-03 1,midg,midg; igrid,midg,midg 5.7833705E-02 6.0958598E-02 gauss-seidel spectral radius is 0.9986755 estimated iterations to convergence 218 setup time was (sec) 0.7600000 now iterating at: 00:40:40 rms-change max change #iterations 4.009089 193.5809 at 10iterations 1.899908 71.89164 at 20iterations 0.8969130 28.38746 at 30iterations 0.4248627 17.58200 at 40iterations 0.2010236 6.017153 at 50iterations 9.5100693E-02 3.130295 at 60iterations 4.4953547E-02 1.531981 at 70iterations 2.1286238E-02 0.6789513 at 80iterations 1.0059724E-02 0.3694115 at 90iterations 4.7662184E-03 0.1507750 at 100iterations 2.2539801E-03 7.4175239E-02 at 110iterations 1.0689592E-03 3.6817551E-02 at 120iterations finished qdiffx linear iterations at : 00:40:46 total time elapsed so far: 6.630000 # loops : 120 mean,max change (kT/e) : 1.0689592E-03 3.6817551E-02 energy calculations done at 6.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.790000 DelPhi exited at 00:40:46 6.793u 0.173s 0:07.26 95.8% 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 00:40:46 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2271 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: 2.933636 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): -0.5390000 54.06900 ymin,ymax (A): -14.51700 27.56900 zmin,zma (A): 30.69700 83.97600 x,y,z range (A): 54.60800 42.08600 53.27900 scale (grids/A): 2.933636 object centre (A): 26.76500 6.526000 57.33650 number of atom coordinates read : 2271 total number of charged atoms : 2137 net assigned charge : 11.50002 assigned positive charge : 332.4886 centred at (gu) : 91.79099 83.53542 85.22230 assigned negative charge : -320.9893 centred at (gu) : 91.90613 83.95140 85.19455 start vw surface at 0.1300000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 163262 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21245 grid for indexing accessible points = 1.400000 m= 81523 mr = 115951 m= 29943 mr = 65378 m= 7532 mr = 23635 m= 1155 mr = 5394 m= 63 mr = 731 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.230000 number of dielectric boundary points 72367 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 17092 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) : 1.955757 object centre at (A) : 26.76500 6.526000 57.33650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2730713 0.6569586 midg,1,midg; midg,igrid,midg 0.4109912 -2.8060911E-02 1,midg,midg; igrid,midg,midg 0.6656098 0.6156603 gauss-seidel spectral radius is 0.9992734 estimated iterations to convergence 293 setup time was (sec) 1.510000 now iterating at: 00:40:48 rms-change max change #iterations 9.520778 404.6534 at 10iterations 5.616303 127.7339 at 20iterations 3.293707 75.02754 at 30iterations 1.923878 37.97495 at 40iterations 1.120070 24.77754 at 50iterations 0.6517481 13.30589 at 60iterations 0.3789368 6.917917 at 70iterations 0.2196292 4.564030 at 80iterations 0.1273135 2.484064 at 90iterations 7.3567167E-02 1.326705 at 100iterations 4.2587537E-02 0.7803802 at 110iterations 2.4666326E-02 0.4596481 at 120iterations 1.4280354E-02 0.2688022 at 130iterations 8.2473559E-03 0.1434917 at 140iterations 4.7670696E-03 9.8026276E-02 at 150iterations 2.7520368E-03 4.9106598E-02 at 160iterations 1.5955328E-03 2.9100418E-02 at 170iterations 9.2195923E-04 1.7475605E-02 at 180iterations finished qdiffx linear iterations at : 00:40:57 total time elapsed so far: 10.84000 # loops : 180 mean,max change (kT/e) : 9.2195923E-04 1.7475605E-02 energy calculations done at 10.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.01000 DelPhi exited at 00:40:58 11.015u 0.178s 0:11.48 97.3% 0+0k 0+0io 0pf+0w