Mon Oct 10 22:03:15 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 Mon Oct 10 2011 at 22:03:15 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 = 2824 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: 0.5608596 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): -26.86300 25.28900 ymin,ymax (A): -33.67800 23.33000 zmin,zma (A): -6.271000 57.20300 x,y,z range (A): 52.15200 57.00800 63.47400 scale (grids/A): 0.5608596 object centre (A): -0.7869997 -5.173999 25.46600 number of atom coordinates read : 2824 total number of charged atoms : 2738 net assigned charge : 0.5000103 assigned positive charge : 415.5342 centred at (gu) : 92.15221 89.30004 90.76588 assigned negative charge : -415.0356 centred at (gu) : 92.06607 89.33517 90.69178 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5923 nv = 96 ne = 84 npr = 55446 no. pairs analyzed = 55446 no. exposed pairs = 3849 no. arc points = 27200 no. surface atoms = 1293 nbur = 1531 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 248 mr = 2927 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3234 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2743 ## 322 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7692 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.3736633E-10 9.6811836E-10 midg,1,midg; midg,igrid,midg 4.6807203E-10 -2.9498343E-10 1,midg,midg; igrid,midg,midg -5.3258192E-10 1.5815466E-09 gauss-seidel spectral radius is 0.9835997 estimated iterations to convergence 64 setup time was (sec) 0.5700000 now iterating at: 22:03:16 rms-change max change #iterations 7.5546458E-02 11.98095 at 10iterations 5.4707523E-03 0.7862835 at 20iterations 4.3538230E-04 7.4413300E-02 at 30iterations 4.1241798E-05 7.5283051E-03 at 40iterations 5.5832202E-06 7.4768066E-04 at 50iterations finished qdiffx linear iterations at : 22:03:19 total time elapsed so far: 4.290000 # loops : 50 mean,max change (kT/e) : 5.5832202E-06 7.4768066E-04 energy calculations done at 4.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.450000 DelPhi exited at 22:03:20 4.457u 0.400s 0:05.42 89.4% 0+0k 0+0io 6pf+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 Mon Oct 10 2011 at 22:03:20 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 = 2824 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: 1.682579 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): -26.86300 25.28900 ymin,ymax (A): -33.67800 23.33000 zmin,zma (A): -6.271000 57.20300 x,y,z range (A): 52.15200 57.00800 63.47400 scale (grids/A): 1.682579 object centre (A): -0.7869997 -5.173999 25.46600 number of atom coordinates read : 2824 total number of charged atoms : 2738 net assigned charge : 0.5000103 assigned positive charge : 415.5342 centred at (gu) : 96.45564 87.89925 92.29700 assigned negative charge : -415.0356 centred at (gu) : 96.19798 88.00536 92.07523 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 65296 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27200 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 19889 mr = 42812 m= 2401 mr = 13459 m= 67 mr = 1224 m= 0 mr = 6 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 80 time to turn everything in is 0.5400000 number of dielectric boundary points 30152 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 251 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 21132 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) : 0.5608596 object centre at (A) : -0.7869997 -5.173999 25.46600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5285386E-02 1.1504147E-02 midg,1,midg; midg,igrid,midg -2.7350099E-03 -8.9638671E-03 1,midg,midg; igrid,midg,midg -7.0302334E-04 2.3986114E-02 gauss-seidel spectral radius is 0.9982880 estimated iterations to convergence 192 setup time was (sec) 0.8500000 now iterating at: 22:03:21 rms-change max change #iterations 3.371842 169.3467 at 10iterations 1.435747 62.47040 at 20iterations 0.6135706 22.31559 at 30iterations 0.2613688 9.454865 at 40iterations 0.1118194 3.961723 at 50iterations 4.7811441E-02 1.847234 at 60iterations 2.0378383E-02 0.7154140 at 70iterations 8.6988090E-03 0.3020282 at 80iterations 3.7402553E-03 0.1397057 at 90iterations 1.5975765E-03 5.9349060E-02 at 100iterations 6.8309676E-04 2.5700569E-02 at 110iterations 2.9258544E-04 1.0234833E-02 at 120iterations finished qdiffx linear iterations at : 22:03:31 total time elapsed so far: 10.15000 # loops : 120 mean,max change (kT/e) : 2.9258544E-04 1.0234833E-02 energy calculations done at 10.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.32000 DelPhi exited at 22:03:31 10.327u 0.441s 0:11.06 97.2% 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 Mon Oct 10 2011 at 22:03:31 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 = 2824 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: 2.523868 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): -26.86300 25.28900 ymin,ymax (A): -33.67800 23.33000 zmin,zma (A): -6.271000 57.20300 x,y,z range (A): 52.15200 57.00800 63.47400 scale (grids/A): 2.523868 object centre (A): -0.7869997 -5.173999 25.46600 number of atom coordinates read : 2824 total number of charged atoms : 2738 net assigned charge : 0.5000103 assigned positive charge : 415.5342 centred at (gu) : 99.68324 86.84867 93.44531 assigned negative charge : -415.0356 centred at (gu) : 99.29690 87.00801 93.11274 start vw surface at 0.1200000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 151539 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27200 grid for indexing accessible points = 1.400000 m= 67465 mr = 105174 m= 20574 mr = 52240 m= 3751 mr = 15356 m= 277 mr = 2585 m= 2 mr = 118 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 290 time to turn everything in is 1.320000 number of dielectric boundary points 68135 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.500000 number of grid points assigned charge 21884 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) : 1.682579 object centre at (A) : -0.7869997 -5.173999 25.46600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5685709 0.2094383 midg,1,midg; midg,igrid,midg -6.2319357E-02 -0.1257324 1,midg,midg; igrid,midg,midg -2.6038099E-02 0.3254886 gauss-seidel spectral radius is 0.9991720 estimated iterations to convergence 274 setup time was (sec) 1.700000 now iterating at: 22:03:33 rms-change max change #iterations 8.697358 432.5643 at 10iterations 4.954342 121.0435 at 20iterations 2.806851 65.26670 at 30iterations 1.582358 32.39225 at 40iterations 0.8876567 21.92520 at 50iterations 0.4969795 10.95483 at 60iterations 0.2773342 6.521086 at 70iterations 0.1552411 3.266988 at 80iterations 8.6333059E-02 1.869128 at 90iterations 4.8206631E-02 1.007546 at 100iterations 2.6818220E-02 0.5630970 at 110iterations 1.4940600E-02 0.3145809 at 120iterations 8.3198305E-03 0.1750708 at 130iterations 4.6247318E-03 9.8281860E-02 at 140iterations 2.5780695E-03 5.0303698E-02 at 150iterations 1.4341351E-03 2.9411316E-02 at 160iterations 7.9992210E-04 1.7410278E-02 at 170iterations 4.4560625E-04 8.4228516E-03 at 180iterations finished qdiffx linear iterations at : 22:03:49 total time elapsed so far: 17.20000 # loops : 180 mean,max change (kT/e) : 4.4560625E-04 8.4228516E-03 energy calculations done at 17.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.37000 DelPhi exited at 22:03:49 17.371u 0.465s 0:18.13 98.3% 0+0k 0+0io 0pf+0w