Tue Oct 11 02:41:28 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 Tue Oct 11 2011 at 02:41:28 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2813 !!! WARNING: FMN 398 has a net charge of -2.0000 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: 0.6660929 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): -22.22300 24.76700 ymin,ymax (A): 10.60900 64.05500 zmin,zma (A): -17.41200 30.29100 x,y,z range (A): 46.99000 53.44600 47.70300 scale (grids/A): 0.6660929 object centre (A): 1.272000 37.33200 6.439500 number of atom coordinates read : 2813 total number of charged atoms : 2679 net assigned charge : 8.000016 assigned positive charge : 434.4842 centred at (gu) : 89.58436 89.67864 90.65891 assigned negative charge : -426.4853 centred at (gu) : 89.71807 89.49574 90.73391 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 8417 nv = 96 ne = 84 npr = 57674 no. pairs analyzed = 57674 no. exposed pairs = 3449 no. arc points = 23471 no. surface atoms = 1152 nbur = 1661 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 458 mr = 4812 m= 7 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 13 time to turn everything in is 0.2400000 number of dielectric boundary points 4000 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2276 ## 210 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9885 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.7648714E-08 5.5159006E-09 midg,1,midg; midg,igrid,midg -2.4870337E-08 6.5222451E-08 1,midg,midg; igrid,midg,midg 6.2773829E-08 -9.2741921E-09 gauss-seidel spectral radius is 0.9883346 estimated iterations to convergence 76 setup time was (sec) 0.4300000 now iterating at: 02:41:28 rms-change max change #iterations 0.1837818 25.10612 at 10iterations 2.1302382E-02 3.461533 at 20iterations 3.7721284E-03 0.6316833 at 30iterations 1.2613111E-03 0.2512207 at 40iterations 4.9724104E-04 9.9136353E-02 at 50iterations finished qdiffx linear iterations at : 02:41:31 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 4.9724104E-04 9.9136353E-02 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 02:41:32 3.463u 0.169s 0:04.44 81.5% 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 Tue Oct 11 2011 at 02:41:32 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2813 !!! WARNING: FMN 398 has a net charge of -2.0000 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: 1.998279 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): -22.22300 24.76700 ymin,ymax (A): 10.60900 64.05500 zmin,zma (A): -17.41200 30.29100 x,y,z range (A): 46.99000 53.44600 47.70300 scale (grids/A): 1.998279 object centre (A): 1.272000 37.33200 6.439500 number of atom coordinates read : 2813 total number of charged atoms : 2679 net assigned charge : 8.000016 assigned positive charge : 434.4842 centred at (gu) : 88.75245 89.03495 91.97605 assigned negative charge : -426.4853 centred at (gu) : 89.15395 88.48677 92.20147 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 90678 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23471 grid for indexing accessible points = 1.400000 m= 34407 mr = 64550 m= 5919 mr = 26109 m= 416 mr = 3927 m= 8 mr = 177 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 1192 time to turn everything in is 0.4400000 number of dielectric boundary points 36665 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 132 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 21176 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) : 0.6660929 object centre at (A) : 1.272000 37.33200 6.439500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.7132787E-03 -2.3904881E-02 midg,1,midg; midg,igrid,midg -4.4651680E-02 8.2831003E-02 1,midg,midg; igrid,midg,midg 6.7829557E-02 2.2244666E-02 gauss-seidel spectral radius is 0.9987758 estimated iterations to convergence 226 setup time was (sec) 0.6500000 now iterating at: 02:41:33 rms-change max change #iterations 4.924010 199.9373 at 10iterations 2.400495 77.80329 at 20iterations 1.173815 33.87974 at 30iterations 0.5704423 17.48436 at 40iterations 0.2799060 8.054140 at 50iterations 0.1364085 4.518518 at 60iterations 6.7043446E-02 1.950226 at 70iterations 3.3062719E-02 1.050674 at 80iterations 1.6618831E-02 0.4703979 at 90iterations 8.6319447E-03 0.3040886 at 100iterations 4.7444799E-03 0.1596222 at 110iterations 2.8110389E-03 0.1037140 at 120iterations finished qdiffx linear iterations at : 02:41:40 total time elapsed so far: 7.820000 # loops : 120 mean,max change (kT/e) : 2.8110389E-03 0.1037140 energy calculations done at 7.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.950000 DelPhi exited at 02:41:41 7.954u 0.219s 0:08.48 96.2% 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 02:41:41 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2813 !!! WARNING: FMN 398 has a net charge of -2.0000 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: 2.997418 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): -22.22300 24.76700 ymin,ymax (A): 10.60900 64.05500 zmin,zma (A): -17.41200 30.29100 x,y,z range (A): 46.99000 53.44600 47.70300 scale (grids/A): 2.997418 object centre (A): 1.272000 37.33200 6.439500 number of atom coordinates read : 2813 total number of charged atoms : 2679 net assigned charge : 8.000016 assigned positive charge : 434.4842 centred at (gu) : 88.12846 88.55211 92.96404 assigned negative charge : -426.4853 centred at (gu) : 88.73092 87.73023 93.30193 start vw surface at 0.1000000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 209511 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23471 grid for indexing accessible points = 1.400000 m= 109740 mr = 155899 m= 41969 mr = 91328 m= 10986 mr = 34317 m= 1818 mr = 8615 m= 123 mr = 1284 m= 3 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 4287 time to turn everything in is 1.160000 number of dielectric boundary points 82656 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 21432 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) : 1.998279 object centre at (A) : 1.272000 37.33200 6.439500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1308667 -0.2759008 midg,1,midg; midg,igrid,midg -0.6122844 1.077262 1,midg,midg; igrid,midg,midg 0.6567307 0.2495545 gauss-seidel spectral radius is 0.9992947 estimated iterations to convergence 297 setup time was (sec) 1.410000 now iterating at: 02:41:42 rms-change max change #iterations 11.23882 422.6124 at 10iterations 6.609218 118.0049 at 20iterations 3.890601 76.27345 at 30iterations 2.280796 46.26254 at 40iterations 1.339229 24.43472 at 50iterations 0.7826225 13.77704 at 60iterations 0.4589108 8.175232 at 70iterations 0.2678774 4.665741 at 80iterations 0.1564561 2.791405 at 90iterations 9.1587208E-02 1.502991 at 100iterations 5.3709202E-02 0.8991623 at 110iterations 3.1503726E-02 0.5182724 at 120iterations 1.8647833E-02 0.3236160 at 130iterations 1.1197078E-02 0.2211227 at 140iterations 6.9144946E-03 0.1449070 at 150iterations 4.4553643E-03 0.1042252 at 160iterations 3.0661977E-03 7.3692322E-02 at 170iterations 2.2532521E-03 5.1246643E-02 at 180iterations finished qdiffx linear iterations at : 02:41:54 total time elapsed so far: 12.98000 # loops : 180 mean,max change (kT/e) : 2.2532521E-03 5.1246643E-02 energy calculations done at 12.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.12000 DelPhi exited at 02:41:55 13.123u 0.205s 0:14.01 95.0% 0+0k 0+0io 0pf+0w