Tue Oct 11 08:23:32 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 08:23:32 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2756 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: SEP 195 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5990341 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): -10.90200 36.75600 ymin,ymax (A): -27.16400 21.77000 zmin,zma (A): -13.55100 45.87800 x,y,z range (A): 47.65800 48.93400 59.42900 scale (grids/A): 0.5990341 object centre (A): 12.92700 -2.697000 16.16350 number of atom coordinates read : 2756 total number of charged atoms : 2606 net assigned charge : -0.8869809 assigned positive charge : 419.0879 centred at (gu) : 89.81710 90.31567 92.34841 assigned negative charge : -419.9753 centred at (gu) : 89.60669 90.17659 92.18525 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 6684 nv = 96 ne = 84 npr = 53785 no. pairs analyzed = 53785 no. exposed pairs = 3437 no. arc points = 24324 no. surface atoms = 1159 nbur = 1597 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 326 mr = 3697 m= 1 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.3900000 number of dielectric boundary points 3287 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2469 ## 267 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 8283 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.0109267E-09 9.7180317E-09 midg,1,midg; midg,igrid,midg -5.4851306E-09 5.0609370E-09 1,midg,midg; igrid,midg,midg -9.1080503E-09 7.0099198E-09 gauss-seidel spectral radius is 0.9855927 estimated iterations to convergence 68 setup time was (sec) 0.6700000 now iterating at: 08:23:33 rms-change max change #iterations 0.1156639 18.54586 at 10iterations 9.9704005E-03 1.569057 at 20iterations 1.0282836E-03 0.1400547 at 30iterations 1.8498882E-04 2.2285461E-02 at 40iterations 5.5376277E-05 8.3446503E-03 at 50iterations finished qdiffx linear iterations at : 08:23:36 total time elapsed so far: 3.860000 # loops : 50 mean,max change (kT/e) : 5.5376277E-05 8.3446503E-03 energy calculations done at 3.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.090000 DelPhi exited at 08:23:37 4.095u 0.150s 0:04.54 93.3% 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 Tue Oct 11 2011 at 08:23:37 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2756 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: SEP 195 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.797102 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): -10.90200 36.75600 ymin,ymax (A): -27.16400 21.77000 zmin,zma (A): -13.55100 45.87800 x,y,z range (A): 47.65800 48.93400 59.42900 scale (grids/A): 1.797102 object centre (A): 12.92700 -2.697000 16.16350 number of atom coordinates read : 2756 total number of charged atoms : 2606 net assigned charge : -0.8869809 assigned positive charge : 419.0879 centred at (gu) : 89.45088 90.94674 97.04482 assigned negative charge : -419.9753 centred at (gu) : 88.81975 90.52946 96.55545 start vw surface at 0.2100000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 72573 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24324 grid for indexing accessible points = 1.400000 m= 26425 mr = 50368 m= 3601 mr = 19631 m= 145 mr = 2174 m= 0 mr = 44 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 747 time to turn everything in is 0.6900000 number of dielectric boundary points 30527 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 200 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 20384 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) : 0.5990341 object centre at (A) : 12.92700 -2.697000 16.16350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.2309105E-02 8.2908862E-04 midg,1,midg; midg,igrid,midg -1.2608852E-02 6.2039755E-03 1,midg,midg; igrid,midg,midg -8.6129764E-03 2.9881550E-02 gauss-seidel spectral radius is 0.9984928 estimated iterations to convergence 204 setup time was (sec) 1.060000 now iterating at: 08:23:38 rms-change max change #iterations 3.985698 192.0661 at 10iterations 1.792955 65.97763 at 20iterations 0.8105843 28.58123 at 30iterations 0.3654286 12.05634 at 40iterations 0.1655171 5.500931 at 50iterations 7.4236125E-02 2.669281 at 60iterations 3.3622790E-02 1.126798 at 70iterations 1.5266293E-02 0.5642328 at 80iterations 6.8606031E-03 0.2191415 at 90iterations 3.1301689E-03 9.8513603E-02 at 100iterations 1.4259485E-03 4.3666840E-02 at 110iterations 6.5859954E-04 2.3427963E-02 at 120iterations finished qdiffx linear iterations at : 08:23:46 total time elapsed so far: 9.420000 # loops : 120 mean,max change (kT/e) : 6.5859954E-04 2.3427963E-02 energy calculations done at 9.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.660000 DelPhi exited at 08:23:47 9.659u 0.251s 0:10.27 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 Tue Oct 11 2011 at 08:23:47 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2756 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: SEP 195 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.695654 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): -10.90200 36.75600 ymin,ymax (A): -27.16400 21.77000 zmin,zma (A): -13.55100 45.87800 x,y,z range (A): 47.65800 48.93400 59.42900 scale (grids/A): 2.695654 object centre (A): 12.92700 -2.697000 16.16350 number of atom coordinates read : 2756 total number of charged atoms : 2606 net assigned charge : -0.8869809 assigned positive charge : 419.0879 centred at (gu) : 89.17616 91.41998 100.5672 assigned negative charge : -419.9753 centred at (gu) : 88.22972 90.79417 99.83318 start vw surface at 0.2000000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 167598 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24324 grid for indexing accessible points = 1.400000 m= 86368 mr = 122018 m= 29750 mr = 71016 m= 6267 mr = 23926 m= 735 mr = 4657 m= 21 mr = 438 m= 0 mr = 0 time to grow re-entrant surface = 0.9899999 no. cavity mid-points inaccessible to solvent = 2376 time to turn everything in is 1.690000 number of dielectric boundary points 68684 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.870000 number of grid points assigned charge 20842 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) : 1.797102 object centre at (A) : 12.92700 -2.697000 16.16350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.387836 0.1056401 midg,1,midg; midg,igrid,midg -0.1555818 3.0790126E-02 1,midg,midg; igrid,midg,midg -6.0084969E-02 0.2923453 gauss-seidel spectral radius is 0.9992213 estimated iterations to convergence 283 setup time was (sec) 2.090000 now iterating at: 08:23:49 rms-change max change #iterations 9.582685 289.7105 at 10iterations 5.507416 155.5607 at 20iterations 3.155216 67.87759 at 30iterations 1.801929 37.28507 at 40iterations 1.027450 19.12665 at 50iterations 0.5857052 11.12817 at 60iterations 0.3326039 6.242120 at 70iterations 0.1894204 3.829287 at 80iterations 0.1077688 2.170746 at 90iterations 6.1061058E-02 1.301732 at 100iterations 3.4751676E-02 0.6435933 at 110iterations 1.9712141E-02 0.3649788 at 120iterations 1.1220997E-02 0.2306824 at 130iterations 6.3989507E-03 0.1188126 at 140iterations 3.6561512E-03 6.7199707E-02 at 150iterations 2.0991683E-03 4.0596008E-02 at 160iterations 1.2117479E-03 2.3529053E-02 at 170iterations 7.1281235E-04 1.3619304E-02 at 180iterations finished qdiffx linear iterations at : 08:24:03 total time elapsed so far: 15.39000 # loops : 180 mean,max change (kT/e) : 7.1281235E-04 1.3619304E-02 energy calculations done at 15.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.63000 DelPhi exited at 08:24:03 15.628u 0.251s 0:16.25 97.6% 0+0k 0+0io 0pf+0w