Mon Oct 10 12:23:22 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 Mon Oct 10 2011 at 12:23:23 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: 239 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2148 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6667916 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): -17.75900 35.63100 ymin,ymax (A): -23.65500 24.86500 zmin,zma (A): -5.328000 45.30300 x,y,z range (A): 53.39000 48.52000 50.63100 scale (grids/A): 0.6667916 object centre (A): 8.935998 0.6050005 19.98750 number of atom coordinates read : 2148 total number of charged atoms : 2007 net assigned charge : -6.999973 assigned positive charge : 322.8239 centred at (gu) : 87.30178 91.61131 86.75916 assigned negative charge : -329.8240 centred at (gu) : 87.57088 91.71040 86.70263 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6375 nv = 96 ne = 84 npr = 44372 no. pairs analyzed = 44372 no. exposed pairs = 2657 no. arc points = 18920 no. surface atoms = 902 nbur = 1246 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 351 mr = 3434 m= 2 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 87 time to turn everything in is 0.2800000 number of dielectric boundary points 3233 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1815 ## 150 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7465 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.3989368E-08 -5.8617924E-09 midg,1,midg; midg,igrid,midg -2.0455098E-09 -5.7422653E-08 1,midg,midg; igrid,midg,midg 5.3604726E-08 -4.3668962E-08 gauss-seidel spectral radius is 0.9883001 estimated iterations to convergence 75 setup time was (sec) 0.5400000 now iterating at: 12:23:24 rms-change max change #iterations 0.1604001 24.00536 at 10iterations 1.7204797E-02 2.576771 at 20iterations 1.8619047E-03 0.2985511 at 30iterations 2.0407297E-04 3.1332016E-02 at 40iterations 2.1724172E-05 3.0670166E-03 at 50iterations finished qdiffx linear iterations at : 12:23:27 total time elapsed so far: 4.480000 # loops : 50 mean,max change (kT/e) : 2.1724172E-05 3.0670166E-03 energy calculations done at 4.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.650000 DelPhi exited at 12:23:28 4.653u 0.422s 0:05.75 88.1% 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 Mon Oct 10 2011 at 12:23:28 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: 239 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2148 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.000375 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): -17.75900 35.63100 ymin,ymax (A): -23.65500 24.86500 zmin,zma (A): -5.328000 45.30300 x,y,z range (A): 53.39000 48.52000 50.63100 scale (grids/A): 2.000375 object centre (A): 8.935998 0.6050005 19.98750 number of atom coordinates read : 2148 total number of charged atoms : 2007 net assigned charge : -6.999973 assigned positive charge : 322.8239 centred at (gu) : 81.90531 94.83379 80.27745 assigned negative charge : -329.8240 centred at (gu) : 82.71256 95.13110 80.10788 start vw surface at 0.1200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 68192 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18920 grid for indexing accessible points = 1.400000 m= 24678 mr = 46426 m= 4178 mr = 18200 m= 280 mr = 2769 m= 2 mr = 127 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 2128 time to turn everything in is 0.5900000 number of dielectric boundary points 29808 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 91 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 15866 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) : 0.6667916 object centre at (A) : 8.935998 0.6050005 19.98750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.3372040E-03 5.4536681E-03 midg,1,midg; midg,igrid,midg 3.4647929E-03 -1.5591153E-02 1,midg,midg; igrid,midg,midg 1.6581468E-02 -6.0060941E-02 gauss-seidel spectral radius is 0.9987013 estimated iterations to convergence 220 setup time was (sec) 0.9200000 now iterating at: 12:23:30 rms-change max change #iterations 4.237885 191.3514 at 10iterations 2.023396 76.88541 at 20iterations 0.9603401 34.24163 at 30iterations 0.4596487 14.31936 at 40iterations 0.2187088 6.980125 at 50iterations 0.1042386 3.233398 at 60iterations 4.9645256E-02 1.667810 at 70iterations 2.3675550E-02 0.7749748 at 80iterations 1.1337993E-02 0.4321327 at 90iterations 5.4019517E-03 0.1767092 at 100iterations 2.5660917E-03 8.4812164E-02 at 110iterations 1.2253973E-03 3.9170265E-02 at 120iterations finished qdiffx linear iterations at : 12:23:39 total time elapsed so far: 10.70000 # loops : 120 mean,max change (kT/e) : 1.2253973E-03 3.9170265E-02 energy calculations done at 10.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.87000 DelPhi exited at 12:23:40 10.877u 0.463s 0:11.75 96.4% 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 12:23:40 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: 239 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2148 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.000562 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): -17.75900 35.63100 ymin,ymax (A): -23.65500 24.86500 zmin,zma (A): -5.328000 45.30300 x,y,z range (A): 53.39000 48.52000 50.63100 scale (grids/A): 3.000562 object centre (A): 8.935998 0.6050005 19.98750 number of atom coordinates read : 2148 total number of charged atoms : 2007 net assigned charge : -6.999973 assigned positive charge : 322.8239 centred at (gu) : 77.85806 97.25070 75.41616 assigned negative charge : -329.8240 centred at (gu) : 79.06889 97.69665 75.16175 start vw surface at 0.1000000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 157545 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18920 grid for indexing accessible points = 1.400000 m= 79036 mr = 112497 m= 29364 mr = 64489 m= 7686 mr = 23776 m= 1319 mr = 6072 m= 64 mr = 935 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.8800001 no. cavity mid-points inaccessible to solvent = 7205 time to turn everything in is 1.500000 number of dielectric boundary points 67216 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.710000 number of grid points assigned charge 16056 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) : 2.000375 object centre at (A) : 8.935998 0.6050005 19.98750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4122470E-02 -9.2522819E-03 midg,1,midg; midg,igrid,midg -1.5481031E-03 -8.4015347E-02 1,midg,midg; igrid,midg,midg 0.4325545 -0.4944834 gauss-seidel spectral radius is 0.9992726 estimated iterations to convergence 293 setup time was (sec) 1.910000 now iterating at: 12:23:43 rms-change max change #iterations 9.791849 406.5211 at 10iterations 5.693854 133.9007 at 20iterations 3.309827 78.70171 at 30iterations 1.912183 40.00790 at 40iterations 1.106610 22.18773 at 50iterations 0.6380464 12.52226 at 60iterations 0.3691009 7.576952 at 70iterations 0.2128386 4.166219 at 80iterations 0.1225726 2.301163 at 90iterations 7.0699550E-02 1.285286 at 100iterations 4.0800527E-02 0.7512341 at 110iterations 2.3495145E-02 0.4048538 at 120iterations 1.3547573E-02 0.2501888 at 130iterations 7.8093810E-03 0.1391392 at 140iterations 4.5054485E-03 8.0463409E-02 at 150iterations 2.5912649E-03 4.9358368E-02 at 160iterations 1.4938401E-03 2.6454210E-02 at 170iterations 8.6400128E-04 1.5316010E-02 at 180iterations finished qdiffx linear iterations at : 12:23:59 total time elapsed so far: 18.47000 # loops : 180 mean,max change (kT/e) : 8.6400128E-04 1.5316010E-02 energy calculations done at 18.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.65000 DelPhi exited at 12:24:00 18.651u 0.506s 0:19.50 98.2% 0+0k 0+0io 0pf+0w