Mon Oct 10 18:46:02 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 Mon Oct 10 2011 at 18:46:02 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 = 2417 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: 0.7001395 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): -14.58300 31.95400 ymin,ymax (A): -6.962000 40.17600 zmin,zma (A): 34.89500 85.74200 x,y,z range (A): 46.53700 47.13800 50.84701 scale (grids/A): 0.7001395 object centre (A): 8.685501 16.60700 60.31850 number of atom coordinates read : 2417 total number of charged atoms : 2280 net assigned charge : 1.000006 assigned positive charge : 359.9708 centred at (gu) : 89.28369 91.67886 88.95161 assigned negative charge : -358.9715 centred at (gu) : 89.42882 91.68008 88.91543 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8384 nv = 96 ne = 84 npr = 48206 no. pairs analyzed = 48206 no. exposed pairs = 3125 no. arc points = 21621 no. surface atoms = 1048 nbur = 1369 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 611 mr = 4738 m= 7 mr = 116 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 4148 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1934 ## 156 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 9089 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3328417E-08 1.9600350E-08 midg,1,midg; midg,igrid,midg 5.3626086E-09 8.4936769E-09 1,midg,midg; igrid,midg,midg 8.7197414E-08 -5.5372425E-08 gauss-seidel spectral radius is 0.9894125 estimated iterations to convergence 79 setup time was (sec) 0.4900000 now iterating at: 18:46:03 rms-change max change #iterations 0.2014569 24.97953 at 10iterations 2.4313210E-02 3.368290 at 20iterations 3.1255146E-03 0.4040451 at 30iterations 4.9538841E-04 7.0926666E-02 at 40iterations 1.3833135E-04 2.1047592E-02 at 50iterations finished qdiffx linear iterations at : 18:46:05 total time elapsed so far: 2.920000 # loops : 50 mean,max change (kT/e) : 1.3833135E-04 2.1047592E-02 energy calculations done at 2.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.100000 DelPhi exited at 18:46:06 3.104u 0.133s 0:03.64 88.7% 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 Mon Oct 10 2011 at 18:46:06 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2417 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.100419 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): -14.58300 31.95400 ymin,ymax (A): -6.962000 40.17600 zmin,zma (A): 34.89500 85.74200 x,y,z range (A): 46.53700 47.13800 50.84701 scale (grids/A): 2.100419 object centre (A): 8.685501 16.60700 60.31850 number of atom coordinates read : 2417 total number of charged atoms : 2280 net assigned charge : 1.000006 assigned positive charge : 359.9708 centred at (gu) : 87.85020 95.03576 86.85397 assigned negative charge : -358.9715 centred at (gu) : 88.28634 95.04004 86.74578 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 88770 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21621 grid for indexing accessible points = 1.400000 m= 36137 mr = 62206 m= 7458 mr = 27299 m= 744 mr = 5036 m= 19 mr = 359 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6100000 number of dielectric boundary points 38228 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 83 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 18090 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) : 0.7001395 object centre at (A) : 8.685501 16.60700 60.31850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0634327E-03 2.7557887E-02 midg,1,midg; midg,igrid,midg -1.0158751E-03 -1.0770990E-02 1,midg,midg; igrid,midg,midg 3.0136803E-02 -1.7470967E-02 gauss-seidel spectral radius is 0.9988534 estimated iterations to convergence 234 setup time was (sec) 0.8700000 now iterating at: 18:46:07 rms-change max change #iterations 4.925241 212.9035 at 10iterations 2.448410 70.11653 at 20iterations 1.226899 35.87154 at 30iterations 0.6124581 17.84801 at 40iterations 0.3065678 8.962374 at 50iterations 0.1530672 4.502975 at 60iterations 7.6816387E-02 2.182243 at 70iterations 3.8266432E-02 1.089024 at 80iterations 1.9120229E-02 0.5819473 at 90iterations 9.6192425E-03 0.2830064 at 100iterations 4.8723686E-03 0.1430492 at 110iterations 2.4893207E-03 7.3303223E-02 at 120iterations finished qdiffx linear iterations at : 18:46:13 total time elapsed so far: 7.010000 # loops : 120 mean,max change (kT/e) : 2.4893207E-03 7.3303223E-02 energy calculations done at 7.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.210000 DelPhi exited at 18:46:14 7.216u 0.175s 0:07.81 94.4% 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 Mon Oct 10 2011 at 18:46:14 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 = 2417 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 3.150628 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): -14.58300 31.95400 ymin,ymax (A): -6.962000 40.17600 zmin,zma (A): 34.89500 85.74200 x,y,z range (A): 46.53700 47.13800 50.84701 scale (grids/A): 3.150628 object centre (A): 8.685501 16.60700 60.31850 number of atom coordinates read : 2417 total number of charged atoms : 2280 net assigned charge : 1.000006 assigned positive charge : 359.9708 centred at (gu) : 86.77504 97.55355 85.28074 assigned negative charge : -358.9715 centred at (gu) : 87.42936 97.55994 85.11856 start vw surface at 0.1800000 fill in re-entrant regions at 0.8900000 boundary points on vw surface= 204662 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21621 grid for indexing accessible points = 1.400000 m= 111186 mr = 149976 m= 46970 mr = 92259 m= 14177 mr = 38526 m= 2980 mr = 11050 m= 315 mr = 2142 m= 4 mr = 180 m= 0 mr = 0 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.980000 number of dielectric boundary points 86161 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.130000 number of grid points assigned charge 18236 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) : 2.100419 object centre at (A) : 8.685501 16.60700 60.31850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1882503 0.6337257 midg,1,midg; midg,igrid,midg -0.1174153 -8.5073426E-02 1,midg,midg; igrid,midg,midg 0.2271679 -0.1708177 gauss-seidel spectral radius is 0.9993165 estimated iterations to convergence 302 setup time was (sec) 2.280000 now iterating at: 18:46:16 rms-change max change #iterations 11.16818 357.3107 at 10iterations 6.699578 141.3640 at 20iterations 4.006325 85.24492 at 30iterations 2.387826 42.53627 at 40iterations 1.419963 26.48840 at 50iterations 0.8415312 15.23891 at 60iterations 0.4973094 8.528761 at 70iterations 0.2942050 4.899136 at 80iterations 0.1733425 3.342968 at 90iterations 0.1023411 1.674742 at 100iterations 6.0124729E-02 0.9949341 at 110iterations 3.5435770E-02 0.5758553 at 120iterations 2.0859202E-02 0.3483868 at 130iterations 1.2294899E-02 0.1920195 at 140iterations 7.2216014E-03 0.1359780 at 150iterations 4.2541744E-03 7.2176337E-02 at 160iterations 2.5026018E-03 3.8807869E-02 at 170iterations 1.4772851E-03 2.3893356E-02 at 180iterations finished qdiffx linear iterations at : 18:46:26 total time elapsed so far: 12.03000 # loops : 180 mean,max change (kT/e) : 1.4772851E-03 2.3893356E-02 energy calculations done at 12.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.20000 DelPhi exited at 18:46:27 12.203u 0.180s 0:12.91 95.8% 0+0k 0+0io 0pf+0w