Sat Oct 8 20:26:08 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 Sat Oct 8 2011 at 20:26:08 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 = 2589 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: 0.6250658 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): -10.75600 38.99900 ymin,ymax (A): -21.89300 24.15900 zmin,zma (A): -12.45000 44.50400 x,y,z range (A): 49.75500 46.05200 56.95400 scale (grids/A): 0.6250658 object centre (A): 14.12150 1.133000 16.02700 number of atom coordinates read : 2589 total number of charged atoms : 2465 net assigned charge : 4.000004 assigned positive charge : 391.9950 centred at (gu) : 88.62209 89.36276 89.85651 assigned negative charge : -387.9955 centred at (gu) : 88.51611 89.40289 89.75170 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6776 nv = 96 ne = 84 npr = 52909 no. pairs analyzed = 52909 no. exposed pairs = 3089 no. arc points = 22222 no. surface atoms = 1028 nbur = 1561 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 316 mr = 3783 m= 2 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 84 time to turn everything in is 0.3500000 number of dielectric boundary points 3272 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2220 ## 211 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8263 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.4061426E-09 1.1453282E-08 midg,1,midg; midg,igrid,midg 7.9677882E-09 7.0258732E-10 1,midg,midg; igrid,midg,midg -6.0205254E-09 8.8257970E-09 gauss-seidel spectral radius is 0.9867421 estimated iterations to convergence 71 setup time was (sec) 0.6300000 now iterating at: 20:26:09 rms-change max change #iterations 0.1285168 18.09858 at 10iterations 1.2306825E-02 1.777973 at 20iterations 1.1553393E-03 0.1625013 at 30iterations 1.1450554E-04 1.8638611E-02 at 40iterations 1.1779497E-05 1.8043518E-03 at 50iterations finished qdiffx linear iterations at : 20:26:12 total time elapsed so far: 3.990000 # loops : 50 mean,max change (kT/e) : 1.1779497E-05 1.8043518E-03 energy calculations done at 3.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.170000 DelPhi exited at 20:26:13 4.169u 0.266s 0:04.70 94.0% 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 Sat Oct 8 2011 at 20:26:13 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 = 2589 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: 1.875197 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): -10.75600 38.99900 ymin,ymax (A): -21.89300 24.15900 zmin,zma (A): -12.45000 44.50400 x,y,z range (A): 49.75500 46.05200 56.95400 scale (grids/A): 1.875197 object centre (A): 14.12150 1.133000 16.02700 number of atom coordinates read : 2589 total number of charged atoms : 2465 net assigned charge : 4.000004 assigned positive charge : 391.9950 centred at (gu) : 85.86590 88.08765 89.56908 assigned negative charge : -387.9955 centred at (gu) : 85.54797 88.20840 89.25499 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 73478 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22222 grid for indexing accessible points = 1.400000 m= 26364 mr = 51501 m= 3780 mr = 19674 m= 199 mr = 2285 m= 0 mr = 56 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 4465 time to turn everything in is 0.6400000 number of dielectric boundary points 30305 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 172 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 19369 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) : 0.6250658 object centre at (A) : 14.12150 1.133000 16.02700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0315696E-02 2.3405930E-02 midg,1,midg; midg,igrid,midg 1.1784475E-02 2.2343174E-03 1,midg,midg; igrid,midg,midg -2.9793591E-03 3.6807232E-02 gauss-seidel spectral radius is 0.9985920 estimated iterations to convergence 211 setup time was (sec) 0.9300000 now iterating at: 20:26:14 rms-change max change #iterations 4.063897 163.6214 at 10iterations 1.880871 80.21230 at 20iterations 0.8703527 27.56523 at 30iterations 0.4025734 13.72808 at 40iterations 0.1867327 6.123471 at 50iterations 8.6577155E-02 2.765900 at 60iterations 4.0081609E-02 1.265093 at 70iterations 1.8561885E-02 0.6278114 at 80iterations 8.5914191E-03 0.2672157 at 90iterations 3.9742128E-03 0.1300278 at 100iterations 1.8434559E-03 6.2526703E-02 at 110iterations 8.5273688E-04 2.8686523E-02 at 120iterations finished qdiffx linear iterations at : 20:26:23 total time elapsed so far: 9.460000 # loops : 120 mean,max change (kT/e) : 8.5273688E-04 2.8686523E-02 energy calculations done at 9.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.650000 DelPhi exited at 20:26:23 9.648u 0.341s 0:10.25 97.3% 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 Sat Oct 8 2011 at 20:26:23 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 = 2589 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: 2.812796 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): -10.75600 38.99900 ymin,ymax (A): -21.89300 24.15900 zmin,zma (A): -12.45000 44.50400 x,y,z range (A): 49.75500 46.05200 56.95400 scale (grids/A): 2.812796 object centre (A): 14.12150 1.133000 16.02700 number of atom coordinates read : 2589 total number of charged atoms : 2465 net assigned charge : 4.000004 assigned positive charge : 391.9950 centred at (gu) : 83.79866 87.13120 89.35357 assigned negative charge : -387.9955 centred at (gu) : 83.32197 87.31246 88.88253 start vw surface at 0.1500000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 169952 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22222 grid for indexing accessible points = 1.400000 m= 86110 mr = 124357 m= 30049 mr = 71306 m= 6746 mr = 24121 m= 839 mr = 4989 m= 46 mr = 529 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 14596 time to turn everything in is 1.640000 number of dielectric boundary points 68430 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.810000 number of grid points assigned charge 19714 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) : 1.875197 object centre at (A) : 14.12150 1.133000 16.02700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1822395 0.2608233 midg,1,midg; midg,igrid,midg 0.1333585 9.2698745E-03 1,midg,midg; igrid,midg,midg -2.0409390E-02 0.4720800 gauss-seidel spectral radius is 0.9992422 estimated iterations to convergence 287 setup time was (sec) 1.980000 now iterating at: 20:26:25 rms-change max change #iterations 9.551203 322.3603 at 10iterations 5.516829 127.8106 at 20iterations 3.160296 75.67539 at 30iterations 1.810221 38.61247 at 40iterations 1.035214 21.16422 at 50iterations 0.5913071 11.91747 at 60iterations 0.3374087 6.125569 at 70iterations 0.1934483 3.582566 at 80iterations 0.1100356 1.960912 at 90iterations 6.2850133E-02 1.185163 at 100iterations 3.5848871E-02 0.6814923 at 110iterations 2.0452853E-02 0.4138393 at 120iterations 1.1665395E-02 0.2138729 at 130iterations 6.6803372E-03 0.1265488 at 140iterations 3.8028138E-03 6.8088531E-02 at 150iterations 2.1710813E-03 4.1637421E-02 at 160iterations 1.2427502E-03 2.2832870E-02 at 170iterations 7.0985581E-04 1.3413429E-02 at 180iterations finished qdiffx linear iterations at : 20:26:39 total time elapsed so far: 15.98000 # loops : 180 mean,max change (kT/e) : 7.0985581E-04 1.3413429E-02 energy calculations done at 15.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.17000 DelPhi exited at 20:26:40 16.169u 0.318s 0:16.76 98.2% 0+0k 0+0io 0pf+0w