Tue Oct 11 08:04:35 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 08:04:35 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3056 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5482236 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): 9.401000 71.95800 ymin,ymax (A): -1.397000 63.54000 zmin,zma (A): -5.290000 37.29200 x,y,z range (A): 62.55700 64.93700 42.58200 scale (grids/A): 0.5482236 object centre (A): 40.67950 31.07150 16.00100 number of atom coordinates read : 3056 total number of charged atoms : 2911 net assigned charge : 11.50002 assigned positive charge : 456.8617 centred at (gu) : 90.60452 91.06708 89.03560 assigned negative charge : -445.3630 centred at (gu) : 90.69115 91.07874 88.95737 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6199 nv = 96 ne = 84 npr = 57785 no. pairs analyzed = 57785 no. exposed pairs = 4195 no. arc points = 30611 no. surface atoms = 1409 nbur = 1647 mkacc time = 0.1600000 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 = 1.568000 m= 272 mr = 2942 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.3400000 number of dielectric boundary points 3523 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3120 ## 402 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 7925 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7084590E-10 1.0687490E-09 midg,1,midg; midg,igrid,midg 6.7844558E-10 9.1308400E-10 1,midg,midg; igrid,midg,midg 1.2170698E-09 1.7893879E-10 gauss-seidel spectral radius is 0.9828672 estimated iterations to convergence 63 setup time was (sec) 0.6900000 now iterating at: 08:04:36 rms-change max change #iterations 7.3289603E-02 12.97519 at 10iterations 4.9141408E-03 0.8195190 at 20iterations 3.2320447E-04 6.0951233E-02 at 30iterations 2.3478113E-05 3.9672852E-03 at 40iterations 2.0378775E-06 2.8991699E-04 at 50iterations finished qdiffx linear iterations at : 08:04:41 total time elapsed so far: 5.180000 # loops : 50 mean,max change (kT/e) : 2.0378775E-06 2.8991699E-04 energy calculations done at 5.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.340000 DelPhi exited at 08:04:41 5.346u 0.444s 0:06.18 93.5% 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 08:04:41 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3056 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.644671 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): 9.401000 71.95800 ymin,ymax (A): -1.397000 63.54000 zmin,zma (A): -5.290000 37.29200 x,y,z range (A): 62.55700 64.93700 42.58200 scale (grids/A): 1.644671 object centre (A): 40.67950 31.07150 16.00100 number of atom coordinates read : 3056 total number of charged atoms : 2911 net assigned charge : 11.50002 assigned positive charge : 456.8617 centred at (gu) : 91.81255 93.20019 87.10588 assigned negative charge : -445.3630 centred at (gu) : 92.07299 93.23562 86.87169 start vw surface at 0.1200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 67662 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30611 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 20248 mr = 43209 m= 2142 mr = 13474 m= 65 mr = 939 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 819 time to turn everything in is 0.5700000 number of dielectric boundary points 32491 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 375 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 22304 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) : 0.5482236 object centre at (A) : 40.67950 31.07150 16.00100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.4677013E-03 5.7377564E-03 midg,1,midg; midg,igrid,midg -1.8937413E-03 -6.7353975E-03 1,midg,midg; igrid,midg,midg 2.6279876E-02 1.0455507E-02 gauss-seidel spectral radius is 0.9982319 estimated iterations to convergence 189 setup time was (sec) 0.9200000 now iterating at: 08:04:43 rms-change max change #iterations 3.380360 158.4099 at 10iterations 1.412969 57.08476 at 20iterations 0.5923664 22.62959 at 30iterations 0.2496772 9.282998 at 40iterations 0.1045869 4.057541 at 50iterations 4.4077542E-02 1.597885 at 60iterations 1.8511694E-02 0.6791673 at 70iterations 7.7756178E-03 0.3034458 at 80iterations 3.2775984E-03 0.1171403 at 90iterations 1.3797334E-03 4.6140671E-02 at 100iterations 5.8041839E-04 2.0702362E-02 at 110iterations 2.4516656E-04 8.8196993E-03 at 120iterations finished qdiffx linear iterations at : 08:04:55 total time elapsed so far: 12.99000 # loops : 120 mean,max change (kT/e) : 2.4516656E-04 8.8196993E-03 energy calculations done at 12.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.16000 DelPhi exited at 08:04:56 13.164u 0.520s 0:14.16 96.6% 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 08:04:56 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3056 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.467006 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): 9.401000 71.95800 ymin,ymax (A): -1.397000 63.54000 zmin,zma (A): -5.290000 37.29200 x,y,z range (A): 62.55700 64.93700 42.58200 scale (grids/A): 2.467006 object centre (A): 40.67950 31.07150 16.00100 number of atom coordinates read : 3056 total number of charged atoms : 2911 net assigned charge : 11.50002 assigned positive charge : 456.8617 centred at (gu) : 92.71877 94.80006 85.65845 assigned negative charge : -445.3630 centred at (gu) : 93.10934 94.85345 85.30750 start vw surface at 0.1300000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 156938 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30611 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 69545 mr = 106352 m= 19798 mr = 53544 m= 3001 mr = 14375 m= 186 mr = 1832 m= 5 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.8200001 no. cavity mid-points inaccessible to solvent = 2736 time to turn everything in is 1.380000 number of dielectric boundary points 73298 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 1.560000 number of grid points assigned charge 23266 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) : 1.644671 object centre at (A) : 40.67950 31.07150 16.00100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1408654 6.7564122E-02 midg,1,midg; midg,igrid,midg -5.5825759E-02 -8.1847444E-02 1,midg,midg; igrid,midg,midg 0.3625700 0.1292672 gauss-seidel spectral radius is 0.9991580 estimated iterations to convergence 272 setup time was (sec) 1.780000 now iterating at: 08:04:58 rms-change max change #iterations 8.849049 325.8534 at 10iterations 5.051941 131.0635 at 20iterations 2.867165 66.02646 at 30iterations 1.613157 36.91003 at 40iterations 0.9025854 18.53422 at 50iterations 0.5039847 11.35862 at 60iterations 0.2807266 6.219685 at 70iterations 0.1561465 2.986869 at 80iterations 8.6818926E-02 1.747773 at 90iterations 4.8184209E-02 1.065376 at 100iterations 2.6700389E-02 0.5431976 at 110iterations 1.4782525E-02 0.2972488 at 120iterations 8.1829783E-03 0.1714714 at 130iterations 4.5233048E-03 0.1003399 at 140iterations 2.5082291E-03 4.9932003E-02 at 150iterations 1.3872492E-03 2.8896332E-02 at 160iterations 7.6641637E-04 1.5857697E-02 at 170iterations 4.2459424E-04 8.0976486E-03 at 180iterations finished qdiffx linear iterations at : 08:05:16 total time elapsed so far: 20.04000 # loops : 180 mean,max change (kT/e) : 4.2459424E-04 8.0976486E-03 energy calculations done at 20.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.21000 DelPhi exited at 08:05:17 20.210u 0.522s 0:21.11 98.1% 0+0k 0+0io 0pf+0w