Tue Oct 11 08:25:46 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 08:25:46 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2768 !!! WARNING: ILE 30 has a net charge of 0.5000 !!! WARNING: HIR 73 has a net charge of 0.5140 !!! WARNING: SEP 228 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6464617 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): -12.23600 36.34300 ymin,ymax (A): -27.13600 21.56800 zmin,zma (A): -9.543000 45.52600 x,y,z range (A): 48.57900 48.70400 55.06900 scale (grids/A): 0.6464617 object centre (A): 12.05350 -2.784000 17.99150 number of atom coordinates read : 2768 total number of charged atoms : 2614 net assigned charge : 5.201013 assigned positive charge : 419.5459 centred at (gu) : 90.57790 90.50710 91.75012 assigned negative charge : -414.3453 centred at (gu) : 90.33808 90.31696 91.73247 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7642 nv = 96 ne = 84 npr = 57357 no. pairs analyzed = 57357 no. exposed pairs = 3157 no. arc points = 21966 no. surface atoms = 1069 nbur = 1699 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 387 mr = 4451 m= 1 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.3400000 number of dielectric boundary points 3520 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2238 ## 218 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9270 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.3137538E-09 1.6300875E-08 midg,1,midg; midg,igrid,midg -1.7860735E-08 4.0381032E-08 1,midg,midg; igrid,midg,midg -2.4372479E-08 4.8942301E-08 gauss-seidel spectral radius is 0.9876085 estimated iterations to convergence 73 setup time was (sec) 0.5900000 now iterating at: 08:25:47 rms-change max change #iterations 0.1600690 23.73090 at 10iterations 1.6605519E-02 2.124374 at 20iterations 1.6886968E-03 0.2306652 at 30iterations 1.8026585E-04 2.4202347E-02 at 40iterations 2.3116449E-05 3.3855438E-03 at 50iterations finished qdiffx linear iterations at : 08:25:51 total time elapsed so far: 4.380000 # loops : 50 mean,max change (kT/e) : 2.3116449E-05 3.3855438E-03 energy calculations done at 4.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.570000 DelPhi exited at 08:25:51 4.570u 0.394s 0:05.27 94.1% 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 08:25:51 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2768 !!! WARNING: ILE 30 has a net charge of 0.5000 !!! WARNING: HIR 73 has a net charge of 0.5140 !!! WARNING: SEP 228 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 1.939385 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): -12.23600 36.34300 ymin,ymax (A): -27.13600 21.56800 zmin,zma (A): -9.543000 45.52600 x,y,z range (A): 48.57900 48.70400 55.06900 scale (grids/A): 1.939385 object centre (A): 12.05350 -2.784000 17.99150 number of atom coordinates read : 2768 total number of charged atoms : 2614 net assigned charge : 5.201013 assigned positive charge : 419.5459 centred at (gu) : 91.73344 91.52094 95.24991 assigned negative charge : -414.3453 centred at (gu) : 91.01386 90.95069 95.19728 start vw surface at 0.1200000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 82353 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21966 grid for indexing accessible points = 1.400000 m= 30956 mr = 59084 m= 5012 mr = 23615 m= 317 mr = 3378 m= 7 mr = 125 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 999 time to turn everything in is 0.6600000 number of dielectric boundary points 32443 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 149 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 20558 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) : 0.6464617 object centre at (A) : 12.05350 -2.784000 17.99150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5448728E-02 1.4476717E-02 midg,1,midg; midg,igrid,midg -1.5228345E-02 2.9841086E-02 1,midg,midg; igrid,midg,midg -3.8836994E-03 6.9425061E-02 gauss-seidel spectral radius is 0.9986910 estimated iterations to convergence 219 setup time was (sec) 0.9600000 now iterating at: 08:25:53 rms-change max change #iterations 4.581627 211.8976 at 10iterations 2.190898 76.10623 at 20iterations 1.044612 33.05550 at 30iterations 0.4969778 14.54778 at 40iterations 0.2364858 7.100231 at 50iterations 0.1131580 3.751312 at 60iterations 5.3965613E-02 1.573780 at 70iterations 2.5685411E-02 0.8668795 at 80iterations 1.2262602E-02 0.3623352 at 90iterations 5.8463369E-03 0.1737809 at 100iterations 2.7948907E-03 8.8529110E-02 at 110iterations 1.3310208E-03 4.2184830E-02 at 120iterations finished qdiffx linear iterations at : 08:26:02 total time elapsed so far: 10.43000 # loops : 120 mean,max change (kT/e) : 1.3310208E-03 4.2184830E-02 energy calculations done at 10.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.60000 DelPhi exited at 08:26:03 10.600u 0.448s 0:11.64 94.8% 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 08:26:03 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2768 !!! WARNING: ILE 30 has a net charge of 0.5000 !!! WARNING: HIR 73 has a net charge of 0.5140 !!! WARNING: SEP 228 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 2.909078 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): -12.23600 36.34300 ymin,ymax (A): -27.13600 21.56800 zmin,zma (A): -9.543000 45.52600 x,y,z range (A): 48.57900 48.70400 55.06900 scale (grids/A): 2.909078 object centre (A): 12.05350 -2.784000 17.99150 number of atom coordinates read : 2768 total number of charged atoms : 2614 net assigned charge : 5.201013 assigned positive charge : 419.5459 centred at (gu) : 92.59988 92.28120 97.87470 assigned negative charge : -414.3453 centred at (gu) : 91.52051 91.42584 97.79580 start vw surface at 0.1400000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 190251 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21966 grid for indexing accessible points = 1.400000 m= 99662 mr = 142197 m= 37028 mr = 83352 m= 9242 mr = 30621 m= 1451 mr = 7220 m= 116 mr = 1053 m= 4 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 3530 time to turn everything in is 1.760000 number of dielectric boundary points 73241 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.900000 number of grid points assigned charge 20910 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) : 1.939385 object centre at (A) : 12.05350 -2.784000 17.99150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3497291 0.3148471 midg,1,midg; midg,igrid,midg -0.1657121 0.3532108 1,midg,midg; igrid,midg,midg -3.5371110E-02 0.5928022 gauss-seidel spectral radius is 0.9992689 estimated iterations to convergence 292 setup time was (sec) 2.080000 now iterating at: 08:26:05 rms-change max change #iterations 10.60491 426.0674 at 10iterations 6.205021 130.0845 at 20iterations 3.618947 70.89388 at 30iterations 2.105319 42.22626 at 40iterations 1.222930 21.77471 at 50iterations 0.7091142 12.93486 at 60iterations 0.4103795 7.071417 at 70iterations 0.2377653 4.001846 at 80iterations 0.1377172 2.568598 at 90iterations 7.9680264E-02 1.550387 at 100iterations 4.6000171E-02 0.8205948 at 110iterations 2.6586251E-02 0.4563828 at 120iterations 1.5327921E-02 0.2546587 at 130iterations 8.8707982E-03 0.1521702 at 140iterations 5.1288106E-03 8.5117340E-02 at 150iterations 2.9657655E-03 4.9234390E-02 at 160iterations 1.7156914E-03 2.8520584E-02 at 170iterations 9.9545834E-04 1.7179489E-02 at 180iterations finished qdiffx linear iterations at : 08:26:22 total time elapsed so far: 18.27000 # loops : 180 mean,max change (kT/e) : 9.9545834E-04 1.7179489E-02 energy calculations done at 18.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.44000 DelPhi exited at 08:26:22 18.441u 0.479s 0:19.22 98.3% 0+0k 0+0io 0pf+0w