Sat Oct 8 14:48:40 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 14:48:40 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3031 !!! WARNING: NAP 500 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6089529 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): -14.70300 36.56100 ymin,ymax (A): -12.27800 46.18300 zmin,zma (A): -40.97000 11.79900 x,y,z range (A): 51.26400 58.46100 52.76900 scale (grids/A): 0.6089529 object centre (A): 10.92900 16.95250 -14.58550 number of atom coordinates read : 3031 total number of charged atoms : 2884 net assigned charge : 7.1674585E-06 assigned positive charge : 453.7835 centred at (gu) : 91.39170 91.31123 91.14528 assigned negative charge : -453.7843 centred at (gu) : 91.44550 91.22258 91.21669 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7272 nv = 96 ne = 84 npr = 63537 no. pairs analyzed = 63537 no. exposed pairs = 3510 no. arc points = 24480 no. surface atoms = 1186 nbur = 1845 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 342 mr = 4179 m= 1 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3407 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2407 ## 262 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9282 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0703109E-09 -5.1853335E-09 midg,1,midg; midg,igrid,midg -3.6882735E-09 6.6558115E-09 1,midg,midg; igrid,midg,midg 2.1980049E-09 -4.1172910E-09 gauss-seidel spectral radius is 0.9860693 estimated iterations to convergence 69 setup time was (sec) 0.5600000 now iterating at: 14:48:41 rms-change max change #iterations 0.1249245 16.57392 at 10iterations 1.1232786E-02 1.495410 at 20iterations 1.0709607E-03 0.1415215 at 30iterations 1.2188994E-04 1.6693115E-02 at 40iterations 1.8550125E-05 2.5165677E-03 at 50iterations finished qdiffx linear iterations at : 14:48:43 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 1.8550125E-05 2.5165677E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 14:48:44 3.468u 0.207s 0:03.96 92.4% 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 14:48:44 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3031 !!! WARNING: NAP 500 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.826859 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): -14.70300 36.56100 ymin,ymax (A): -12.27800 46.18300 zmin,zma (A): -40.97000 11.79900 x,y,z range (A): 51.26400 58.46100 52.76900 scale (grids/A): 1.826859 object centre (A): 10.92900 16.95250 -14.58550 number of atom coordinates read : 3031 total number of charged atoms : 2884 net assigned charge : 7.1674585E-06 assigned positive charge : 453.7835 centred at (gu) : 94.17458 93.93333 93.43542 assigned negative charge : -453.7843 centred at (gu) : 94.33634 93.66763 93.64990 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 80691 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24480 grid for indexing accessible points = 1.400000 m= 27477 mr = 57811 m= 3546 mr = 20225 m= 134 mr = 2005 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.5800000 number of dielectric boundary points 31772 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 176 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 22598 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) : 0.6089529 object centre at (A) : 10.92900 16.95250 -14.58550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4657690E-02 1.1586238E-03 midg,1,midg; midg,igrid,midg -1.3314039E-02 3.0574424E-02 1,midg,midg; igrid,midg,midg 7.8500304E-03 -1.2762665E-02 gauss-seidel spectral radius is 0.9985553 estimated iterations to convergence 209 setup time was (sec) 0.8800000 now iterating at: 14:48:45 rms-change max change #iterations 4.275692 166.6289 at 10iterations 1.959240 62.80965 at 20iterations 0.9019240 29.42821 at 30iterations 0.4130996 12.79720 at 40iterations 0.1901155 5.620987 at 50iterations 8.7335043E-02 3.163628 at 60iterations 4.0147662E-02 1.311586 at 70iterations 1.8398987E-02 0.5494461 at 80iterations 8.4642870E-03 0.2393570 at 90iterations 3.9017766E-03 0.1167507 at 100iterations 1.7910119E-03 5.2604675E-02 at 110iterations 8.2170533E-04 2.6138306E-02 at 120iterations finished qdiffx linear iterations at : 14:48:52 total time elapsed so far: 7.740000 # loops : 120 mean,max change (kT/e) : 8.2170533E-04 2.6138306E-02 energy calculations done at 7.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.920000 DelPhi exited at 14:48:52 7.919u 0.235s 0:08.49 95.8% 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 Sat Oct 8 2011 at 14:48:53 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3031 !!! WARNING: NAP 500 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.740288 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): -14.70300 36.56100 ymin,ymax (A): -12.27800 46.18300 zmin,zma (A): -40.97000 11.79900 x,y,z range (A): 51.26400 58.46100 52.76900 scale (grids/A): 2.740288 object centre (A): 10.92900 16.95250 -14.58550 number of atom coordinates read : 3031 total number of charged atoms : 2884 net assigned charge : 7.1674585E-06 assigned positive charge : 453.7835 centred at (gu) : 96.26160 95.89981 95.15280 assigned negative charge : -453.7843 centred at (gu) : 96.50445 95.50164 95.47483 start vw surface at 0.1600000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 187306 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24480 grid for indexing accessible points = 1.400000 m= 92533 mr = 140072 m= 29867 mr = 76417 m= 5873 mr = 23518 m= 587 mr = 4172 m= 20 mr = 321 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 35 time to turn everything in is 1.430000 number of dielectric boundary points 71682 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.570000 number of grid points assigned charge 23069 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) : 1.826859 object centre at (A) : 10.92900 16.95250 -14.58550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1497725 0.1487045 midg,1,midg; midg,igrid,midg -9.6019723E-02 0.3925757 1,midg,midg; igrid,midg,midg 0.1284070 -0.1084749 gauss-seidel spectral radius is 0.9992397 estimated iterations to convergence 286 setup time was (sec) 1.750000 now iterating at: 14:48:54 rms-change max change #iterations 10.17028 271.5715 at 10iterations 5.907199 132.9395 at 20iterations 3.405130 75.36018 at 30iterations 1.967010 43.52749 at 40iterations 1.127809 22.58387 at 50iterations 0.6468416 12.37830 at 60iterations 0.3696874 6.735824 at 70iterations 0.2116083 3.786010 at 80iterations 0.1213270 2.103507 at 90iterations 6.9431044E-02 1.180328 at 100iterations 3.9596114E-02 0.6967010 at 110iterations 2.2656020E-02 0.3827209 at 120iterations 1.2949789E-02 0.2299213 at 130iterations 7.3916488E-03 0.1306515 at 140iterations 4.2216238E-03 8.1167221E-02 at 150iterations 2.4138524E-03 4.1873932E-02 at 160iterations 1.3808645E-03 2.3975372E-02 at 170iterations 7.9314510E-04 1.3412476E-02 at 180iterations finished qdiffx linear iterations at : 14:49:06 total time elapsed so far: 13.01000 # loops : 180 mean,max change (kT/e) : 7.9314510E-04 1.3412476E-02 energy calculations done at 13.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.18000 DelPhi exited at 14:49:06 13.186u 0.226s 0:13.70 97.8% 0+0k 0+0io 0pf+0w