Tue Oct 11 06:03:16 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 06:03:16 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 0.7045877 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): 25.72000 72.08800 ymin,ymax (A): -18.93400 31.59200 zmin,zma (A): 4.023000 46.35600 x,y,z range (A): 46.36800 50.52600 42.33300 scale (grids/A): 0.7045877 object centre (A): 48.90400 6.329000 25.18950 number of atom coordinates read : 2327 total number of charged atoms : 2000 net assigned charge : 6.039011 assigned positive charge : 327.3059 centred at (gu) : 89.24618 90.20556 90.36604 assigned negative charge : -321.2671 centred at (gu) : 89.37473 90.14429 90.44975 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7185 nv = 96 ne = 84 npr = 42746 no. pairs analyzed = 42746 no. exposed pairs = 2624 no. arc points = 17673 no. surface atoms = 898 nbur = 1429 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 468 mr = 4144 m= 2 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3435 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1637 ## 158 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7975 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.0947494E-08 7.2336150E-09 midg,1,midg; midg,igrid,midg 1.7197847E-08 7.9420907E-08 1,midg,midg; igrid,midg,midg 1.2503860E-07 -1.2488362E-08 gauss-seidel spectral radius is 0.9895038 estimated iterations to convergence 79 setup time was (sec) 0.5000000 now iterating at: 06:03:17 rms-change max change #iterations 0.2014260 36.44015 at 10iterations 2.5519229E-02 2.941231 at 20iterations 3.6955108E-03 0.4667206 at 30iterations 7.7451835E-04 9.6664429E-02 at 40iterations 2.2848426E-04 2.3849487E-02 at 50iterations finished qdiffx linear iterations at : 06:03:20 total time elapsed so far: 3.130000 # loops : 50 mean,max change (kT/e) : 2.2848426E-04 2.3849487E-02 energy calculations done at 3.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.290000 DelPhi exited at 06:03:20 3.298u 0.215s 0:03.84 91.1% 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 06:03:20 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 2.113763 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): 25.72000 72.08800 ymin,ymax (A): -18.93400 31.59200 zmin,zma (A): 4.023000 46.35600 x,y,z range (A): 46.36800 50.52600 42.33300 scale (grids/A): 2.113763 object centre (A): 48.90400 6.329000 25.18950 number of atom coordinates read : 2327 total number of charged atoms : 2000 net assigned charge : 6.039011 assigned positive charge : 327.3059 centred at (gu) : 87.73878 90.61668 91.09801 assigned negative charge : -321.2671 centred at (gu) : 88.12424 90.43285 91.34935 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 75966 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17673 grid for indexing accessible points = 1.400000 m= 30855 mr = 54217 m= 5849 mr = 23410 m= 478 mr = 3879 m= 23 mr = 215 m= 0 mr = 4 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 31446 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 86 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 15853 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) : 0.7045877 object centre at (A) : 48.90400 6.329000 25.18950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8739996E-02 2.5959719E-02 midg,1,midg; midg,igrid,midg 4.1169237E-02 2.7799301E-02 1,midg,midg; igrid,midg,midg 4.3072313E-02 -4.4979613E-02 gauss-seidel spectral radius is 0.9988262 estimated iterations to convergence 231 setup time was (sec) 0.8400000 now iterating at: 06:03:21 rms-change max change #iterations 4.657106 167.8973 at 10iterations 2.297802 75.28592 at 20iterations 1.140141 35.54742 at 30iterations 0.5649028 15.94489 at 40iterations 0.2801023 8.665459 at 50iterations 0.1389453 4.018014 at 60iterations 6.8998434E-02 2.181839 at 70iterations 3.4443054E-02 0.9801979 at 80iterations 1.7318195E-02 0.5316658 at 90iterations 8.7865777E-03 0.2579199 at 100iterations 4.5160125E-03 0.1361160 at 110iterations 2.4280339E-03 7.3059082E-02 at 120iterations finished qdiffx linear iterations at : 06:03:28 total time elapsed so far: 6.970000 # loops : 120 mean,max change (kT/e) : 2.4280339E-03 7.3059082E-02 energy calculations done at 6.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.140000 DelPhi exited at 06:03:28 7.142u 0.186s 0:07.86 93.1% 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 06:03:28 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 3.170645 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): 25.72000 72.08800 ymin,ymax (A): -18.93400 31.59200 zmin,zma (A): 4.023000 46.35600 x,y,z range (A): 46.36800 50.52600 42.33300 scale (grids/A): 3.170645 object centre (A): 48.90400 6.329000 25.18950 number of atom coordinates read : 2327 total number of charged atoms : 2000 net assigned charge : 6.039011 assigned positive charge : 327.3059 centred at (gu) : 86.60803 90.92492 91.64708 assigned negative charge : -321.2671 centred at (gu) : 87.18636 90.64930 92.02406 start vw surface at 0.1600000 fill in re-entrant regions at 0.8200000 boundary points on vw surface= 175159 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17673 grid for indexing accessible points = 1.400000 m= 96087 mr = 130589 m= 38840 mr = 79888 m= 10913 mr = 31931 m= 2025 mr = 8457 m= 236 mr = 1409 m= 17 mr = 134 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.8699999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.810000 number of dielectric boundary points 70864 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.960000 number of grid points assigned charge 16000 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) : 2.113763 object centre at (A) : 48.90400 6.329000 25.18950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1145704 0.2213780 midg,1,midg; midg,igrid,midg 0.3029492 0.1411875 1,midg,midg; igrid,midg,midg 0.4245879 -0.5717805 gauss-seidel spectral radius is 0.9992965 estimated iterations to convergence 297 setup time was (sec) 2.130000 now iterating at: 06:03:31 rms-change max change #iterations 10.43062 331.7411 at 10iterations 6.175465 128.3655 at 20iterations 3.665172 83.85023 at 30iterations 2.160449 45.03790 at 40iterations 1.271815 23.10198 at 50iterations 0.7487922 14.92386 at 60iterations 0.4404128 8.056799 at 70iterations 0.2582111 4.330143 at 80iterations 0.1513792 2.617676 at 90iterations 8.8918567E-02 1.627686 at 100iterations 5.2377492E-02 0.8692551 at 110iterations 3.0986553E-02 0.5511246 at 120iterations 1.8485449E-02 0.3528900 at 130iterations 1.1201154E-02 0.2038307 at 140iterations 6.9735558E-03 0.1292419 at 150iterations 4.5253769E-03 8.4815979E-02 at 160iterations 3.1213374E-03 5.7769775E-02 at 170iterations 2.2797380E-03 4.5848846E-02 at 180iterations finished qdiffx linear iterations at : 06:03:42 total time elapsed so far: 13.27000 # loops : 180 mean,max change (kT/e) : 2.2797380E-03 4.5848846E-02 energy calculations done at 13.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.45000 DelPhi exited at 06:03:42 13.448u 0.241s 0:14.20 96.3% 0+0k 0+0io 0pf+0w