Sat Oct 8 12:53:54 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 Sat Oct 8 2011 at 12:53:54 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1288 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7073035 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): 0.2500000 40.64700 ymin,ymax (A): -4.345000 35.82400 zmin,zma (A): -15.55600 34.77600 x,y,z range (A): 40.39700 40.16900 50.33200 scale (grids/A): 0.7073035 object centre (A): 20.44850 15.73950 9.610001 number of atom coordinates read : 1288 total number of charged atoms : 1152 net assigned charge : 1.000011 assigned positive charge : 189.0983 centred at (gu) : 90.49741 89.03221 90.69353 assigned negative charge : -188.0980 centred at (gu) : 90.58468 88.87643 90.18367 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 4452 nv = 96 ne = 84 npr = 25416 no. pairs analyzed = 25416 no. exposed pairs = 1658 no. arc points = 12187 no. surface atoms = 563 nbur = 725 mkacc time = 5.0000012E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 269 mr = 2278 m= 2 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 5.0000012E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 2401 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1000 ## 82 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 4604 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3140429E-07 1.7484747E-07 midg,1,midg; midg,igrid,midg -4.7037354E-08 4.4549076E-08 1,midg,midg; igrid,midg,midg 3.0869817E-08 -1.9695346E-08 gauss-seidel spectral radius is 0.9895114 estimated iterations to convergence 79 setup time was (sec) 0.4200000 now iterating at: 12:53:54 rms-change max change #iterations 0.1536534 29.95787 at 10iterations 1.8454993E-02 3.212905 at 20iterations 2.2499955E-03 0.3814316 at 30iterations 2.6929830E-04 4.5883179E-02 at 40iterations 3.2721829E-05 5.6877136E-03 at 50iterations finished qdiffx linear iterations at : 12:53:57 total time elapsed so far: 3.010000 # loops : 50 mean,max change (kT/e) : 3.2721829E-05 5.6877136E-03 energy calculations done at 3.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.180000 DelPhi exited at 12:53:58 3.184u 0.168s 0:03.65 91.5% 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 Sat Oct 8 2011 at 12:53:58 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 = 1288 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.121911 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): 0.2500000 40.64700 ymin,ymax (A): -4.345000 35.82400 zmin,zma (A): -15.55600 34.77600 x,y,z range (A): 40.39700 40.16900 50.33200 scale (grids/A): 2.121911 object centre (A): 20.44850 15.73950 9.610001 number of atom coordinates read : 1288 total number of charged atoms : 1152 net assigned charge : 1.000011 assigned positive charge : 189.0983 centred at (gu) : 91.49244 87.09688 92.08076 assigned negative charge : -188.0980 centred at (gu) : 91.75393 86.62920 90.55079 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 46837 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12187 grid for indexing accessible points = 1.400000 m= 16628 mr = 30631 m= 3166 mr = 11916 m= 334 mr = 2063 m= 11 mr = 188 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 22178 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 60 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9151 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) : 0.7073035 object centre at (A) : 20.44850 15.73950 9.610001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3876749E-02 9.5653079E-02 midg,1,midg; midg,igrid,midg -2.7582724E-02 9.7849267E-03 1,midg,midg; igrid,midg,midg 4.9753045E-04 -4.4137007E-03 gauss-seidel spectral radius is 0.9987583 estimated iterations to convergence 225 setup time was (sec) 0.6500000 now iterating at: 12:53:58 rms-change max change #iterations 3.590584 211.8524 at 10iterations 1.715641 80.54333 at 20iterations 0.8341241 31.55307 at 30iterations 0.4026278 16.28276 at 40iterations 0.1954709 7.266104 at 50iterations 9.3868658E-02 3.995938 at 60iterations 4.5508076E-02 1.914520 at 70iterations 2.1971243E-02 0.8778830 at 80iterations 1.0603493E-02 0.4085693 at 90iterations 5.1530055E-03 0.1955566 at 100iterations 2.4975357E-03 9.7427368E-02 at 110iterations 1.2104317E-03 4.5417786E-02 at 120iterations finished qdiffx linear iterations at : 12:54:05 total time elapsed so far: 6.980000 # loops : 120 mean,max change (kT/e) : 1.2104317E-03 4.5417786E-02 energy calculations done at 6.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.160000 DelPhi exited at 12:54:05 7.163u 0.202s 0:07.66 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 Sat Oct 8 2011 at 12:54:05 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 = 1288 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.182866 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): 0.2500000 40.64700 ymin,ymax (A): -4.345000 35.82400 zmin,zma (A): -15.55600 34.77600 x,y,z range (A): 40.39700 40.16900 50.33200 scale (grids/A): 3.182866 object centre (A): 20.44850 15.73950 9.610001 number of atom coordinates read : 1288 total number of charged atoms : 1152 net assigned charge : 1.000011 assigned positive charge : 189.0983 centred at (gu) : 92.23887 85.64531 93.12117 assigned negative charge : -188.0980 centred at (gu) : 92.63083 84.94384 90.82623 start vw surface at 0.1300000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 107831 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12187 grid for indexing accessible points = 1.400000 m= 52622 mr = 74303 m= 20107 mr = 42156 m= 5935 mr = 16004 m= 1351 mr = 4521 m= 177 mr = 1008 m= 5 mr = 126 m= 0 mr = 0 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.110000 number of dielectric boundary points 49910 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.240000 number of grid points assigned charge 9216 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) : 2.121911 object centre at (A) : 20.44850 15.73950 9.610001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.3167307E-02 0.9527127 midg,1,midg; midg,igrid,midg -0.2817151 0.1036469 1,midg,midg; igrid,midg,midg -1.4440593E-04 -2.6213497E-02 gauss-seidel spectral radius is 0.9992728 estimated iterations to convergence 293 setup time was (sec) 1.410000 now iterating at: 12:54:07 rms-change max change #iterations 8.006470 502.5718 at 10iterations 4.583032 120.8607 at 20iterations 2.639758 72.21816 at 30iterations 1.514628 37.49639 at 40iterations 0.8706501 18.54007 at 50iterations 0.5013272 11.38233 at 60iterations 0.2883682 6.456345 at 70iterations 0.1659970 3.867213 at 80iterations 9.5501706E-02 2.111813 at 90iterations 5.4773171E-02 1.236668 at 100iterations 3.1523515E-02 0.6492076 at 110iterations 1.8117614E-02 0.4110603 at 120iterations 1.0408900E-02 0.2139235 at 130iterations 5.9966287E-03 0.1246066 at 140iterations 3.4511203E-03 7.7916145E-02 at 150iterations 1.9874638E-03 4.4794083E-02 at 160iterations 1.1458946E-03 2.3849487E-02 at 170iterations 6.5926014E-04 1.3948441E-02 at 180iterations finished qdiffx linear iterations at : 12:54:17 total time elapsed so far: 11.37000 # loops : 180 mean,max change (kT/e) : 6.5926014E-04 1.3948441E-02 energy calculations done at 11.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.55000 DelPhi exited at 12:54:17 11.556u 0.189s 0:12.04 97.4% 0+0k 0+0io 0pf+0w