Sat Oct 8 11:34:54 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 11:34:54 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3365 !!! WARNING: HIZ 15 has a net charge of 0.2000 !!! WARNING: HIZ 17 has a net charge of 0.2000 !!! WARNING: HIZ 214 has a net charge of 0.2000 !!! WARNING: ZN5 540 has a net charge of 1.4000 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: 0.6209013 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): 32.36200 81.13400 ymin,ymax (A): 24.54100 81.87700 zmin,zma (A): -3.070000 46.38700 x,y,z range (A): 48.77200 57.33600 49.45700 scale (grids/A): 0.6209013 object centre (A): 56.74800 53.20900 21.65850 number of atom coordinates read : 3365 total number of charged atoms : 3214 net assigned charge : -3.999964 assigned positive charge : 513.3683 centred at (gu) : 90.69398 89.68325 91.19492 assigned negative charge : -517.3693 centred at (gu) : 90.49073 89.77644 91.19520 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8231 nv = 96 ne = 84 npr = 71753 no. pairs analyzed = 71753 no. exposed pairs = 3723 no. arc points = 25474 no. surface atoms = 1276 nbur = 2089 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 462 mr = 4883 m= 4 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 145 time to turn everything in is 0.3500000 number of dielectric boundary points 3772 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2521 ## 249 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 10382 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.6626961E-09 -4.4947490E-09 midg,1,midg; midg,igrid,midg 5.3007638E-09 -1.1196653E-08 1,midg,midg; igrid,midg,midg -1.9155214E-08 1.7093326E-08 gauss-seidel spectral radius is 0.9866187 estimated iterations to convergence 71 setup time was (sec) 0.5500000 now iterating at: 11:34:54 rms-change max change #iterations 0.1521585 26.55406 at 10iterations 1.4478597E-02 1.891586 at 20iterations 1.3449142E-03 0.2384396 at 30iterations 1.2814099E-04 1.6556263E-02 at 40iterations 1.2904043E-05 1.7929077E-03 at 50iterations finished qdiffx linear iterations at : 11:34:57 total time elapsed so far: 2.980000 # loops : 50 mean,max change (kT/e) : 1.2904043E-05 1.7929077E-03 energy calculations done at 2.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.150000 DelPhi exited at 11:34:58 3.153u 0.158s 0:03.96 83.3% 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 11:34:58 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3365 !!! WARNING: HIZ 15 has a net charge of 0.2000 !!! WARNING: HIZ 17 has a net charge of 0.2000 !!! WARNING: HIZ 214 has a net charge of 0.2000 !!! WARNING: ZN5 540 has a net charge of 1.4000 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: 1.862704 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): 32.36200 81.13400 ymin,ymax (A): 24.54100 81.87700 zmin,zma (A): -3.070000 46.38700 x,y,z range (A): 48.77200 57.33600 49.45700 scale (grids/A): 1.862704 object centre (A): 56.74800 53.20900 21.65850 number of atom coordinates read : 3365 total number of charged atoms : 3214 net assigned charge : -3.999964 assigned positive charge : 513.3683 centred at (gu) : 92.08105 89.04871 93.58402 assigned negative charge : -517.3693 centred at (gu) : 91.47163 89.32886 93.58504 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 89939 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25474 grid for indexing accessible points = 1.400000 m= 33288 mr = 65032 m= 5280 mr = 25638 m= 234 mr = 3455 m= 2 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 7527 time to turn everything in is 0.6100000 number of dielectric boundary points 34551 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 173 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 25195 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) : 0.6209013 object centre at (A) : 56.74800 53.20900 21.65850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6353298E-02 -2.8677946E-02 midg,1,midg; midg,igrid,midg 1.8632889E-02 -2.4002008E-02 1,midg,midg; igrid,midg,midg -3.3908628E-02 2.3328736E-02 gauss-seidel spectral radius is 0.9986333 estimated iterations to convergence 214 setup time was (sec) 0.8700000 now iterating at: 11:34:59 rms-change max change #iterations 4.822384 208.8493 at 10iterations 2.258169 74.51517 at 20iterations 1.056554 30.06800 at 30iterations 0.4954343 16.59321 at 40iterations 0.2324214 7.876404 at 50iterations 0.1089305 3.024452 at 60iterations 5.1015206E-02 1.449768 at 70iterations 2.3908082E-02 0.7281914 at 80iterations 1.1246189E-02 0.3238239 at 90iterations 5.2985274E-03 0.1499786 at 100iterations 2.4846105E-03 7.3715210E-02 at 110iterations 1.1618430E-03 3.6872864E-02 at 120iterations finished qdiffx linear iterations at : 11:35:05 total time elapsed so far: 6.920000 # loops : 120 mean,max change (kT/e) : 1.1618430E-03 3.6872864E-02 energy calculations done at 6.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.100000 DelPhi exited at 11:35:05 7.101u 0.169s 0:07.72 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 11:35:06 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3365 !!! WARNING: HIZ 15 has a net charge of 0.2000 !!! WARNING: HIZ 17 has a net charge of 0.2000 !!! WARNING: HIZ 214 has a net charge of 0.2000 !!! WARNING: ZN5 540 has a net charge of 1.4000 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: 2.794056 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): 32.36200 81.13400 ymin,ymax (A): 24.54100 81.87700 zmin,zma (A): -3.070000 46.38700 x,y,z range (A): 48.77200 57.33600 49.45700 scale (grids/A): 2.794056 object centre (A): 56.74800 53.20900 21.65850 number of atom coordinates read : 3365 total number of charged atoms : 3214 net assigned charge : -3.999964 assigned positive charge : 513.3683 centred at (gu) : 93.12122 88.57280 95.37578 assigned negative charge : -517.3693 centred at (gu) : 92.20747 88.99319 95.37743 start vw surface at 0.1700000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 208492 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25474 grid for indexing accessible points = 1.400000 m= 107294 mr = 156968 m= 40289 mr = 89969 m= 9681 mr = 33771 m= 1183 mr = 7508 m= 48 mr = 769 m= 0 mr = 7 time to grow re-entrant surface = 0.9200001 no. cavity mid-points inaccessible to solvent = 25610 time to turn everything in is 1.610000 number of dielectric boundary points 77995 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.750000 number of grid points assigned charge 25710 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) : 1.862704 object centre at (A) : 56.74800 53.20900 21.65850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1917168 -0.2193519 midg,1,midg; midg,igrid,midg 0.1966638 2.0716345E-02 1,midg,midg; igrid,midg,midg -0.3384850 0.2915992 gauss-seidel spectral radius is 0.9992604 estimated iterations to convergence 290 setup time was (sec) 1.910000 now iterating at: 11:35:08 rms-change max change #iterations 11.07592 346.6557 at 10iterations 6.434468 121.3252 at 20iterations 3.710979 64.11858 at 30iterations 2.141143 37.49599 at 40iterations 1.235052 20.98300 at 50iterations 0.7096160 12.68088 at 60iterations 0.4080481 7.121520 at 70iterations 0.2344121 3.682613 at 80iterations 0.1347520 2.315781 at 90iterations 7.7406168E-02 1.292794 at 100iterations 4.4471573E-02 0.7567978 at 110iterations 2.5574114E-02 0.4535764 at 120iterations 1.4695836E-02 0.2438889 at 130iterations 8.4425313E-03 0.1471939 at 140iterations 4.8541753E-03 8.2550049E-02 at 150iterations 2.7943044E-03 4.6760559E-02 at 160iterations 1.6037149E-03 2.5943995E-02 at 170iterations 9.2244137E-04 1.4549255E-02 at 180iterations finished qdiffx linear iterations at : 11:35:19 total time elapsed so far: 12.96000 # loops : 180 mean,max change (kT/e) : 9.2244137E-04 1.4549255E-02 energy calculations done at 12.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.14000 DelPhi exited at 11:35:19 13.142u 0.247s 0:13.91 96.1% 0+0k 0+0io 0pf+0w