Sun Oct 9 22:32:19 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 Sun Oct 9 2011 at 22:32:19 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 = 3108 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: 0.5610009 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): -17.30200 42.77500 ymin,ymax (A): -5.811000 57.64700 zmin,zma (A): -5.212000 47.32100 x,y,z range (A): 60.07700 63.45800 52.53300 scale (grids/A): 0.5610009 object centre (A): 12.73650 25.91800 21.05450 number of atom coordinates read : 3108 total number of charged atoms : 3037 net assigned charge : 4.500007 assigned positive charge : 480.2220 centred at (gu) : 89.15094 88.27027 89.56066 assigned negative charge : -475.7229 centred at (gu) : 89.23214 88.21288 89.53147 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6601 nv = 96 ne = 84 npr = 57875 no. pairs analyzed = 57875 no. exposed pairs = 4481 no. arc points = 32365 no. surface atoms = 1475 nbur = 1633 mkacc time = 0.1000000 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= 329 mr = 3138 m= 0 mr = 7 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3785 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3272 ## 421 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8587 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5634420E-10 7.7175466E-10 midg,1,midg; midg,igrid,midg -3.3203271E-10 7.9346157E-10 1,midg,midg; igrid,midg,midg 1.8246347E-09 -4.0378387E-10 gauss-seidel spectral radius is 0.9836345 estimated iterations to convergence 64 setup time was (sec) 0.4100000 now iterating at: 22:32:19 rms-change max change #iterations 8.4928676E-02 15.10464 at 10iterations 6.0065789E-03 0.8883476 at 20iterations 4.3788936E-04 7.5218201E-02 at 30iterations 3.5422901E-05 5.4283142E-03 at 40iterations 4.7358576E-06 6.7424774E-04 at 50iterations finished qdiffx linear iterations at : 22:32:22 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 4.7358576E-06 6.7424774E-04 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 22:32:23 3.462u 0.176s 0:03.90 93.0% 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 Sun Oct 9 2011 at 22:32:23 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 = 3108 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: 1.683003 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): -17.30200 42.77500 ymin,ymax (A): -5.811000 57.64700 zmin,zma (A): -5.212000 47.32100 x,y,z range (A): 60.07700 63.45800 52.53300 scale (grids/A): 1.683003 object centre (A): 12.73650 25.91800 21.05450 number of atom coordinates read : 3108 total number of charged atoms : 3037 net assigned charge : 4.500007 assigned positive charge : 480.2220 centred at (gu) : 87.45187 84.81050 88.68140 assigned negative charge : -475.7229 centred at (gu) : 87.69577 84.63832 88.59379 start vw surface at 0.1200000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 72092 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32365 grid for indexing accessible points = 1.400000 m= 22582 mr = 46178 m= 2738 mr = 14968 m= 120 mr = 1259 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 238 time to turn everything in is 0.3700000 number of dielectric boundary points 35107 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 323 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 23424 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) : 0.5610009 object centre at (A) : 12.73650 25.91800 21.05450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.9925577E-03 4.5170416E-03 midg,1,midg; midg,igrid,midg 8.7552043E-03 -5.0868276E-03 1,midg,midg; igrid,midg,midg -1.1001012E-03 3.5867658E-03 gauss-seidel spectral radius is 0.9983360 estimated iterations to convergence 195 setup time was (sec) 0.5900000 now iterating at: 22:32:23 rms-change max change #iterations 3.659972 147.5109 at 10iterations 1.570834 51.30592 at 20iterations 0.6777260 26.14718 at 30iterations 0.2910505 11.15185 at 40iterations 0.1254253 4.422199 at 50iterations 5.4161124E-02 1.851456 at 60iterations 2.3397271E-02 0.8277512 at 70iterations 1.0114977E-02 0.3382072 at 80iterations 4.3678707E-03 0.1462708 at 90iterations 1.8884167E-03 6.8763375E-02 at 100iterations 8.1716967E-04 3.0554771E-02 at 110iterations 3.5330484E-04 1.3412476E-02 at 120iterations finished qdiffx linear iterations at : 22:32:31 total time elapsed so far: 7.780000 # loops : 120 mean,max change (kT/e) : 3.5330484E-04 1.3412476E-02 energy calculations done at 7.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.910000 DelPhi exited at 22:32:31 7.916u 0.188s 0:08.45 95.7% 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 Sun Oct 9 2011 at 22:32:31 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 = 3108 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: 2.524504 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): -17.30200 42.77500 ymin,ymax (A): -5.811000 57.64700 zmin,zma (A): -5.212000 47.32100 x,y,z range (A): 60.07700 63.45800 52.53300 scale (grids/A): 2.524504 object centre (A): 12.73650 25.91800 21.05450 number of atom coordinates read : 3108 total number of charged atoms : 3037 net assigned charge : 4.500007 assigned positive charge : 480.2220 centred at (gu) : 86.17772 82.21546 88.02192 assigned negative charge : -475.7229 centred at (gu) : 86.54359 81.95727 87.89048 start vw surface at 0.1000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 167261 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32365 grid for indexing accessible points = 1.400000 m= 76474 mr = 114019 m= 23096 mr = 58693 m= 4369 mr = 16745 m= 434 mr = 2686 m= 14 mr = 194 m= 0 mr = 4 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 837 time to turn everything in is 0.8700000 number of dielectric boundary points 79307 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 24282 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) : 1.683003 object centre at (A) : 12.73650 25.91800 21.05450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1230766 7.4640885E-02 midg,1,midg; midg,igrid,midg 4.8546400E-02 -0.1946885 1,midg,midg; igrid,midg,midg -0.1558105 3.1978402E-02 gauss-seidel spectral radius is 0.9992014 estimated iterations to convergence 279 setup time was (sec) 1.100000 now iterating at: 22:32:33 rms-change max change #iterations 9.532854 337.9313 at 10iterations 5.565329 169.1216 at 20iterations 3.230085 85.72124 at 30iterations 1.856264 44.86545 at 40iterations 1.064996 25.57896 at 50iterations 0.6066279 14.24905 at 60iterations 0.3456008 7.333702 at 70iterations 0.1960899 4.294182 at 80iterations 0.1111017 2.288307 at 90iterations 6.2764198E-02 1.255236 at 100iterations 3.5480518E-02 0.7466578 at 110iterations 2.0003706E-02 0.4370012 at 120iterations 1.1288426E-02 0.2486248 at 130iterations 6.3664238E-03 0.1214337 at 140iterations 3.5815162E-03 7.2733164E-02 at 150iterations 2.0183236E-03 4.3831214E-02 at 160iterations 1.1343438E-03 2.1511078E-02 at 170iterations 6.3921255E-04 1.3369560E-02 at 180iterations finished qdiffx linear iterations at : 22:32:44 total time elapsed so far: 12.58000 # loops : 180 mean,max change (kT/e) : 6.3921255E-04 1.3369560E-02 energy calculations done at 12.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.72000 DelPhi exited at 22:32:44 12.726u 0.207s 0:13.25 97.5% 0+0k 0+0io 0pf+0w