Sat Oct 15 13:19:30 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 15 2011 at 13:19:33 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 = 3175 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: 0.6611816 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): -8.995000 44.84800 ymin,ymax (A): -13.73700 38.90500 zmin,zma (A): 38.00400 90.21900 x,y,z range (A): 53.84300 52.64200 52.21500 scale (grids/A): 0.6611816 object centre (A): 17.92650 12.58400 64.11150 number of atom coordinates read : 3175 total number of charged atoms : 3027 net assigned charge : 4.500015 assigned positive charge : 481.0887 centred at (gu) : 91.09274 90.65566 88.81070 assigned negative charge : -476.5901 centred at (gu) : 91.11419 90.67907 88.90250 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 9426 nv = 96 ne = 84 npr = 62806 no. pairs analyzed = 62806 no. exposed pairs = 4195 no. arc points = 29943 no. surface atoms = 1387 nbur = 1788 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 552 mr = 4921 m= 6 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 92 time to turn everything in is 0.4000000 number of dielectric boundary points 4988 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2835 ## 235 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 11047 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.3995250E-08 -8.8713437E-09 midg,1,midg; midg,igrid,midg 1.5246107E-08 6.4804118E-09 1,midg,midg; igrid,midg,midg 1.3572182E-08 7.6581932E-09 gauss-seidel spectral radius is 0.9882060 estimated iterations to convergence 75 setup time was (sec) 0.6800000 now iterating at: 13:19:34 rms-change max change #iterations 0.1871812 25.35610 at 10iterations 1.9732026E-02 2.454071 at 20iterations 2.1349445E-03 0.3030281 at 30iterations 2.3880554E-04 3.4027100E-02 at 40iterations 3.4621738E-05 4.5022964E-03 at 50iterations finished qdiffx linear iterations at : 13:19:41 total time elapsed so far: 4.080000 # loops : 50 mean,max change (kT/e) : 3.4621738E-05 4.5022964E-03 energy calculations done at 4.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.270000 DelPhi exited at 13:19:42 4.272u 0.293s 0:09.55 47.7% 0+0k 0+0io 6pf+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 15 2011 at 13:19:42 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 = 3175 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: 1.983545 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): -8.995000 44.84800 ymin,ymax (A): -13.73700 38.90500 zmin,zma (A): 38.00400 90.21900 x,y,z range (A): 53.84300 52.64200 52.21500 scale (grids/A): 1.983545 object centre (A): 17.92650 12.58400 64.11150 number of atom coordinates read : 3175 total number of charged atoms : 3027 net assigned charge : 4.500015 assigned positive charge : 481.0887 centred at (gu) : 93.27744 91.96635 86.43144 assigned negative charge : -476.5901 centred at (gu) : 93.34231 92.03700 86.70713 start vw surface at 0.1700000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 100844 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29943 grid for indexing accessible points = 1.400000 m= 36648 mr = 68214 m= 6446 mr = 26312 m= 530 mr = 3940 m= 11 mr = 217 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 2727 time to turn everything in is 0.8800000 number of dielectric boundary points 45796 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 142 iepsmp to db, and charging done at 1.040000 number of grid points assigned charge 23934 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) : 0.6611816 object centre at (A) : 17.92650 12.58400 64.11150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9366687E-02 -6.5327045E-03 midg,1,midg; midg,igrid,midg 1.7426095E-03 -1.1932680E-02 1,midg,midg; igrid,midg,midg 1.5911661E-02 4.0912546E-02 gauss-seidel spectral radius is 0.9988047 estimated iterations to convergence 229 setup time was (sec) 1.220000 now iterating at: 13:19:46 rms-change max change #iterations 5.141544 198.1569 at 10iterations 2.528962 70.73745 at 20iterations 1.241130 34.44987 at 30iterations 0.6095582 16.87308 at 40iterations 0.2997104 8.634384 at 50iterations 0.1470352 4.465722 at 60iterations 7.2252393E-02 2.052769 at 70iterations 3.5670411E-02 1.000243 at 80iterations 1.7478680E-02 0.5005841 at 90iterations 8.5883476E-03 0.2306976 at 100iterations 4.2273374E-03 0.1115503 at 110iterations 2.0829036E-03 5.8077812E-02 at 120iterations finished qdiffx linear iterations at : 13:20:12 total time elapsed so far: 10.13000 # loops : 120 mean,max change (kT/e) : 2.0829036E-03 5.8077812E-02 energy calculations done at 10.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.32000 DelPhi exited at 13:20:14 10.325u 0.319s 0:31.96 33.2% 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 15 2011 at 13:20:19 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 = 3175 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: 2.975317 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): -8.995000 44.84800 ymin,ymax (A): -13.73700 38.90500 zmin,zma (A): 38.00400 90.21900 x,y,z range (A): 53.84300 52.64200 52.21500 scale (grids/A): 2.975317 object centre (A): 17.92650 12.58400 64.11150 number of atom coordinates read : 3175 total number of charged atoms : 3027 net assigned charge : 4.500015 assigned positive charge : 481.0887 centred at (gu) : 94.91589 92.94925 84.64697 assigned negative charge : -476.5901 centred at (gu) : 95.01324 93.05538 85.06082 start vw surface at 0.1800000 fill in re-entrant regions at 0.7500000 boundary points on vw surface= 232905 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29943 grid for indexing accessible points = 1.400000 m= 117039 mr = 165435 m= 43672 mr = 94520 m= 11902 mr = 34254 m= 2072 mr = 8722 m= 171 mr = 1428 m= 2 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 1.450000 no. cavity mid-points inaccessible to solvent = 8615 time to turn everything in is 2.350000 number of dielectric boundary points 103332 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.520000 number of grid points assigned charge 24216 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) : 1.983545 object centre at (A) : 17.92650 12.58400 64.11150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1651625 -2.3211518E-02 midg,1,midg; midg,igrid,midg -1.2108578E-02 -0.3345368 1,midg,midg; igrid,midg,midg 0.1394560 0.2430777 gauss-seidel spectral radius is 0.9993321 estimated iterations to convergence 305 setup time was (sec) 2.710000 now iterating at: 13:20:30 rms-change max change #iterations 12.05778 370.0089 at 10iterations 7.333559 162.0362 at 20iterations 4.436900 93.77525 at 30iterations 2.681893 56.99696 at 40iterations 1.604579 29.49851 at 50iterations 0.9630502 19.11845 at 60iterations 0.5736845 11.36091 at 70iterations 0.3427885 6.277519 at 80iterations 0.2037737 3.196121 at 90iterations 0.1212330 2.021267 at 100iterations 7.2073191E-02 1.233475 at 110iterations 4.2884275E-02 0.7277508 at 120iterations 2.5392596E-02 0.3857946 at 130iterations 1.5107594E-02 0.2759452 at 140iterations 8.9571700E-03 0.1449585 at 150iterations 5.3225723E-03 9.5383078E-02 at 160iterations 3.1520566E-03 5.0331354E-02 at 170iterations 1.8721771E-03 2.8721929E-02 at 180iterations finished qdiffx linear iterations at : 13:21:15 total time elapsed so far: 17.68000 # loops : 180 mean,max change (kT/e) : 1.8721771E-03 2.8721929E-02 energy calculations done at 17.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.86000 DelPhi exited at 13:21:16 17.858u 0.324s 0:57.91 31.3% 0+0k 0+0io 0pf+0w