Tue Oct 11 08:22:48 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 Tue Oct 11 2011 at 08:22:48 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2800 !!! WARNING: HIR 71 has a net charge of 0.5140 !!! WARNING: SEP 226 has a net charge of -0.4750 !!! 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.6598458 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): -9.562000 36.86600 ymin,ymax (A): -27.49000 21.70900 zmin,zma (A): -8.268000 45.68400 x,y,z range (A): 46.42800 49.19900 53.95200 scale (grids/A): 0.6598458 object centre (A): 13.65200 -2.890500 18.70800 number of atom coordinates read : 2800 total number of charged atoms : 2646 net assigned charge : 3.701017 assigned positive charge : 424.6659 centred at (gu) : 89.42302 90.53115 91.03359 assigned negative charge : -420.9652 centred at (gu) : 89.12042 90.38798 91.03263 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 8187 nv = 96 ne = 84 npr = 57144 no. pairs analyzed = 57144 no. exposed pairs = 3332 no. arc points = 22979 no. surface atoms = 1127 nbur = 1673 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 448 mr = 4756 m= 2 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 26 time to turn everything in is 0.3600000 number of dielectric boundary points 3817 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2263 ## 212 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9687 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.7437878E-09 1.2240565E-08 midg,1,midg; midg,igrid,midg -1.8979673E-08 4.4522046E-08 1,midg,midg; igrid,midg,midg -6.4527299E-08 6.4029777E-08 gauss-seidel spectral radius is 0.9881102 estimated iterations to convergence 75 setup time was (sec) 0.6100000 now iterating at: 08:22:49 rms-change max change #iterations 0.1770278 21.51635 at 10iterations 1.9254355E-02 2.332636 at 20iterations 2.2131361E-03 0.2512817 at 30iterations 3.5721555E-04 4.5921326E-02 at 40iterations 9.3876974E-05 9.7990036E-03 at 50iterations finished qdiffx linear iterations at : 08:22:52 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 9.3876974E-05 9.7990036E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 08:22:52 3.467u 0.129s 0:04.08 87.7% 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 08:22:52 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2800 !!! WARNING: HIR 71 has a net charge of 0.5140 !!! WARNING: SEP 226 has a net charge of -0.4750 !!! 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.979537 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): -9.562000 36.86600 ymin,ymax (A): -27.49000 21.70900 zmin,zma (A): -8.268000 45.68400 x,y,z range (A): 46.42800 49.19900 53.95200 scale (grids/A): 1.979537 object centre (A): 13.65200 -2.890500 18.70800 number of atom coordinates read : 2800 total number of charged atoms : 2646 net assigned charge : 3.701017 assigned positive charge : 424.6659 centred at (gu) : 88.26860 91.59307 93.10024 assigned negative charge : -420.9652 centred at (gu) : 87.36111 91.16351 93.09764 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 88278 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22979 grid for indexing accessible points = 1.400000 m= 33940 mr = 63337 m= 5548 mr = 25908 m= 385 mr = 3611 m= 9 mr = 182 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 936 time to turn everything in is 0.6500000 number of dielectric boundary points 35122 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 135 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 20903 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) : 0.6598458 object centre at (A) : 13.65200 -2.890500 18.70800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2934375E-03 5.7687964E-03 midg,1,midg; midg,igrid,midg -1.2343867E-02 3.3846065E-02 1,midg,midg; igrid,midg,midg -2.5760558E-02 6.9056988E-02 gauss-seidel spectral radius is 0.9987485 estimated iterations to convergence 224 setup time was (sec) 0.9400000 now iterating at: 08:22:54 rms-change max change #iterations 4.840075 269.5192 at 10iterations 2.350659 73.44601 at 20iterations 1.135584 32.10796 at 30iterations 0.5510020 19.07041 at 40iterations 0.2676077 7.474980 at 50iterations 0.1295957 3.753836 at 60iterations 6.2922768E-02 1.763710 at 70iterations 3.0541671E-02 0.9317532 at 80iterations 1.4774537E-02 0.4155741 at 90iterations 7.1881269E-03 0.1919098 at 100iterations 3.4944077E-03 0.1181183 at 110iterations 1.7008951E-03 5.0175667E-02 at 120iterations finished qdiffx linear iterations at : 08:23:00 total time elapsed so far: 7.820000 # loops : 120 mean,max change (kT/e) : 1.7008951E-03 5.0175667E-02 energy calculations done at 7.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.000000 DelPhi exited at 08:23:01 8.001u 0.223s 0:08.70 94.4% 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 Tue Oct 11 2011 at 08:23:01 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2800 !!! WARNING: HIR 71 has a net charge of 0.5140 !!! WARNING: SEP 226 has a net charge of -0.4750 !!! 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.969306 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): -9.562000 36.86600 ymin,ymax (A): -27.49000 21.70900 zmin,zma (A): -8.268000 45.68400 x,y,z range (A): 46.42800 49.19900 53.95200 scale (grids/A): 2.969306 object centre (A): 13.65200 -2.890500 18.70800 number of atom coordinates read : 2800 total number of charged atoms : 2646 net assigned charge : 3.701017 assigned positive charge : 424.6659 centred at (gu) : 87.40258 92.38963 94.65026 assigned negative charge : -420.9652 centred at (gu) : 86.04147 91.74522 94.64639 start vw surface at 0.1500000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 203615 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22979 grid for indexing accessible points = 1.400000 m= 108616 mr = 152459 m= 41332 mr = 90733 m= 10166 mr = 34050 m= 1703 mr = 7902 m= 135 mr = 1264 m= 2 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 3309 time to turn everything in is 1.670000 number of dielectric boundary points 79086 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.820000 number of grid points assigned charge 21168 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) : 1.979537 object centre at (A) : 13.65200 -2.890500 18.70800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4103514E-03 0.2732136 midg,1,midg; midg,igrid,midg -0.1566273 0.3779337 1,midg,midg; igrid,midg,midg -0.1681923 0.6062278 gauss-seidel spectral radius is 0.9992854 estimated iterations to convergence 295 setup time was (sec) 1.990000 now iterating at: 08:23:03 rms-change max change #iterations 11.01000 385.7891 at 10iterations 6.489434 160.0397 at 20iterations 3.808591 70.31104 at 30iterations 2.233986 40.00027 at 40iterations 1.303810 24.10683 at 50iterations 0.7635328 14.16975 at 60iterations 0.4454310 8.535501 at 70iterations 0.2603880 5.209488 at 80iterations 0.1517416 2.541965 at 90iterations 8.8443674E-02 1.575821 at 100iterations 5.1542416E-02 0.8249321 at 110iterations 3.0043645E-02 0.5082703 at 120iterations 1.7535068E-02 0.3396397 at 130iterations 1.0280642E-02 0.1790009 at 140iterations 6.0572908E-03 9.5015526E-02 at 150iterations 3.6057280E-03 6.1781883E-02 at 160iterations 2.1810404E-03 4.1347504E-02 at 170iterations 1.3549996E-03 2.2706985E-02 at 180iterations finished qdiffx linear iterations at : 08:23:15 total time elapsed so far: 13.85000 # loops : 180 mean,max change (kT/e) : 1.3549996E-03 2.2706985E-02 energy calculations done at 13.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.08000 DelPhi exited at 08:23:17 14.079u 0.240s 0:15.29 93.5% 0+0k 0+0io 0pf+0w