Tue Oct 11 06:24:13 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 06:24:13 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 = 1316 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.8045016 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): -14.81400 25.53000 ymin,ymax (A): 42.62400 76.67400 zmin,zma (A): -4.691000 39.56000 x,y,z range (A): 40.34400 34.05000 44.25100 scale (grids/A): 0.8045016 object centre (A): 5.358001 59.64899 17.43450 number of atom coordinates read : 1316 total number of charged atoms : 1268 net assigned charge : 2.500002 assigned positive charge : 201.4374 centred at (gu) : 90.05686 90.01338 89.82191 assigned negative charge : -198.9373 centred at (gu) : 90.18589 90.07570 89.53860 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6377 nv = 96 ne = 84 npr = 24440 no. pairs analyzed = 24440 no. exposed pairs = 1736 no. arc points = 12357 no. surface atoms = 603 nbur = 713 mkacc time = 5.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 580 mr = 3640 m= 7 mr = 132 m= 0 mr = 0 time to grow re-entrant surface = 7.0000000E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3192 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 869 ## 73 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 6033 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.6840566E-07 7.2498921E-07 midg,1,midg; midg,igrid,midg 2.9318173E-07 2.9760596E-08 1,midg,midg; igrid,midg,midg 4.2859227E-07 -1.1538288E-07 gauss-seidel spectral radius is 0.9918618 estimated iterations to convergence 90 setup time was (sec) 0.4000000 now iterating at: 06:24:13 rms-change max change #iterations 0.2651139 40.60869 at 10iterations 4.0849309E-02 5.307899 at 20iterations 6.5475786E-03 0.9127541 at 30iterations 1.0210378E-03 0.1356316 at 40iterations 1.7474892E-04 2.3796082E-02 at 50iterations finished qdiffx linear iterations at : 06:24:16 total time elapsed so far: 2.850000 # loops : 50 mean,max change (kT/e) : 1.7474892E-04 2.3796082E-02 energy calculations done at 2.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.030000 DelPhi exited at 06:24:17 3.038u 0.162s 0:03.78 84.3% 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 06:24:17 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 = 1316 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: 2.413505 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): -14.81400 25.53000 ymin,ymax (A): 42.62400 76.67400 zmin,zma (A): -4.691000 39.56000 x,y,z range (A): 40.34400 34.05000 44.25100 scale (grids/A): 2.413505 object centre (A): 5.358001 59.64899 17.43450 number of atom coordinates read : 1316 total number of charged atoms : 1268 net assigned charge : 2.500002 assigned positive charge : 201.4374 centred at (gu) : 90.17080 90.04034 89.46587 assigned negative charge : -198.9373 centred at (gu) : 90.55784 90.22729 88.61595 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 65979 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12357 grid for indexing accessible points = 1.400000 m= 29270 mr = 45887 m= 7616 mr = 22778 m= 977 mr = 5503 m= 61 mr = 548 m= 1 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 29161 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 10121 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) : 0.8045016 object centre at (A) : 5.358001 59.64899 17.43450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.9362904E-02 7.1721688E-02 midg,1,midg; midg,igrid,midg 2.4040617E-02 4.8661842E-03 1,midg,midg; igrid,midg,midg 7.4944474E-02 1.3190712E-02 gauss-seidel spectral radius is 0.9989966 estimated iterations to convergence 250 setup time was (sec) 0.7700000 now iterating at: 06:24:18 rms-change max change #iterations 4.522383 224.5260 at 10iterations 2.368387 83.87485 at 20iterations 1.237855 42.30835 at 30iterations 0.6441413 19.63588 at 40iterations 0.3361001 10.38609 at 50iterations 0.1760474 5.329712 at 60iterations 9.1685213E-02 2.603054 at 70iterations 4.8054591E-02 1.435771 at 80iterations 2.5005048E-02 0.7430191 at 90iterations 1.3086473E-02 0.4048405 at 100iterations 6.8598082E-03 0.1915379 at 110iterations 3.6047054E-03 0.1110640 at 120iterations finished qdiffx linear iterations at : 06:24:24 total time elapsed so far: 6.800000 # loops : 120 mean,max change (kT/e) : 3.6047054E-03 0.1110640 energy calculations done at 6.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.970000 DelPhi exited at 06:24:24 6.977u 0.177s 0:07.61 93.8% 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 06:24:24 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 = 1316 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.620257 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): -14.81400 25.53000 ymin,ymax (A): 42.62400 76.67400 zmin,zma (A): -4.691000 39.56000 x,y,z range (A): 40.34400 34.05000 44.25100 scale (grids/A): 3.620257 object centre (A): 5.358001 59.64899 17.43450 number of atom coordinates read : 1316 total number of charged atoms : 1268 net assigned charge : 2.500002 assigned positive charge : 201.4374 centred at (gu) : 90.25632 90.06058 89.19890 assigned negative charge : -198.9373 centred at (gu) : 90.83688 90.34090 87.92402 start vw surface at 0.1200000 fill in re-entrant regions at 0.6800000 boundary points on vw surface= 151334 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12357 grid for indexing accessible points = 1.400000 m= 86358 mr = 109976 m= 41452 mr = 72478 m= 15166 mr = 35024 m= 3834 mr = 12309 m= 627 mr = 2906 m= 82 mr = 427 m= 1 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.600000 number of dielectric boundary points 65677 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 10144 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) : 2.413505 object centre at (A) : 5.358001 59.64899 17.43450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6352344 0.4589554 midg,1,midg; midg,igrid,midg 0.1451485 4.0274154E-02 1,midg,midg; igrid,midg,midg 0.5620486 1.1482074E-02 gauss-seidel spectral radius is 0.9993290 estimated iterations to convergence 305 setup time was (sec) 1.880000 now iterating at: 06:24:26 rms-change max change #iterations 9.622587 288.4309 at 10iterations 5.809540 132.1800 at 20iterations 3.488613 73.50918 at 30iterations 2.093533 48.12495 at 40iterations 1.245575 26.96352 at 50iterations 0.7432024 13.99471 at 60iterations 0.4420541 9.848940 at 70iterations 0.2625788 5.299139 at 80iterations 0.1561780 2.967903 at 90iterations 9.2765220E-02 1.658890 at 100iterations 5.5020131E-02 1.004101 at 110iterations 3.2630157E-02 0.7309151 at 120iterations 1.9321945E-02 0.3722115 at 130iterations 1.1468418E-02 0.2159954 at 140iterations 6.7935139E-03 0.1259489 at 150iterations 4.0473435E-03 7.1777344E-02 at 160iterations 2.4246124E-03 4.8666000E-02 at 170iterations 1.4758047E-03 2.9928207E-02 at 180iterations finished qdiffx linear iterations at : 06:24:36 total time elapsed so far: 11.36000 # loops : 180 mean,max change (kT/e) : 1.4758047E-03 2.9928207E-02 energy calculations done at 11.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.54000 DelPhi exited at 06:24:36 11.548u 0.192s 0:12.15 96.5% 0+0k 0+0io 0pf+0w