Tue Oct 11 07:48:43 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 Tue Oct 11 2011 at 07:48:43 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2763 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: 0.6344228 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): -13.54100 42.57300 ymin,ymax (A): -21.71000 28.57700 zmin,zma (A): -11.63400 40.51300 x,y,z range (A): 56.11400 50.28700 52.14700 scale (grids/A): 0.6344228 object centre (A): 14.51600 3.433499 14.43950 number of atom coordinates read : 2763 total number of charged atoms : 2400 net assigned charge : 10.50002 assigned positive charge : 385.5691 centred at (gu) : 90.06866 87.65551 90.84846 assigned negative charge : -375.0697 centred at (gu) : 90.04366 87.60392 91.06658 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6710 nv = 96 ne = 84 npr = 51553 no. pairs analyzed = 51553 no. exposed pairs = 2990 no. arc points = 20650 no. surface atoms = 1017 nbur = 1746 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 326 mr = 3794 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3202 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2108 ## 249 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8136 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8111906E-08 -1.0019976E-08 midg,1,midg; midg,igrid,midg 1.3385106E-08 1.1157785E-08 1,midg,midg; igrid,midg,midg 1.0714980E-08 1.5894068E-08 gauss-seidel spectral radius is 0.9871165 estimated iterations to convergence 72 setup time was (sec) 0.4000000 now iterating at: 07:48:44 rms-change max change #iterations 0.1427645 19.09100 at 10iterations 1.4286443E-02 2.057384 at 20iterations 1.5861499E-03 0.2356110 at 30iterations 2.3813974E-04 4.0630341E-02 at 40iterations 4.8143531E-05 7.4653625E-03 at 50iterations finished qdiffx linear iterations at : 07:48:47 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 4.8143531E-05 7.4653625E-03 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 07:48:47 3.437u 0.172s 0:03.96 90.9% 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 07:48:47 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2763 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: 1.903268 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): -13.54100 42.57300 ymin,ymax (A): -21.71000 28.57700 zmin,zma (A): -11.63400 40.51300 x,y,z range (A): 56.11400 50.28700 52.14700 scale (grids/A): 1.903268 object centre (A): 14.51600 3.433499 14.43950 number of atom coordinates read : 2763 total number of charged atoms : 2400 net assigned charge : 10.50002 assigned positive charge : 385.5691 centred at (gu) : 90.20554 82.96603 92.54478 assigned negative charge : -375.0697 centred at (gu) : 90.13086 82.81157 93.19971 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 72081 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20650 grid for indexing accessible points = 1.400000 m= 26309 mr = 50849 m= 3924 mr = 19838 m= 223 mr = 2485 m= 4 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 757 time to turn everything in is 0.3600000 number of dielectric boundary points 29294 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 198 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 18867 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) : 0.6344228 object centre at (A) : 14.51600 3.433499 14.43950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5509858E-02 -9.1589168E-03 midg,1,midg; midg,igrid,midg 1.5113206E-02 2.5591318E-02 1,midg,midg; igrid,midg,midg 2.1430884E-02 4.5669533E-02 gauss-seidel spectral radius is 0.9986160 estimated iterations to convergence 213 setup time was (sec) 0.5800000 now iterating at: 07:48:48 rms-change max change #iterations 4.132937 188.0905 at 10iterations 1.930257 63.88815 at 20iterations 0.9010217 29.55985 at 30iterations 0.4209740 13.77253 at 40iterations 0.1970470 6.307056 at 50iterations 9.1952920E-02 2.800257 at 60iterations 4.3021329E-02 1.414320 at 70iterations 2.0082662E-02 0.6156387 at 80iterations 9.4614914E-03 0.3122921 at 90iterations 4.4421987E-03 0.1523650 at 100iterations 2.0954509E-03 7.1426392E-02 at 110iterations 1.0059926E-03 3.4555435E-02 at 120iterations finished qdiffx linear iterations at : 07:48:55 total time elapsed so far: 7.740000 # loops : 120 mean,max change (kT/e) : 1.0059926E-03 3.4555435E-02 energy calculations done at 7.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.880000 DelPhi exited at 07:48:56 7.884u 0.198s 0:08.59 93.9% 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 07:48:56 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2763 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: 2.854903 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): -13.54100 42.57300 ymin,ymax (A): -21.71000 28.57700 zmin,zma (A): -11.63400 40.51300 x,y,z range (A): 56.11400 50.28700 52.14700 scale (grids/A): 2.854903 object centre (A): 14.51600 3.433499 14.43950 number of atom coordinates read : 2763 total number of charged atoms : 2400 net assigned charge : 10.50002 assigned positive charge : 385.5691 centred at (gu) : 90.30820 79.44902 93.81706 assigned negative charge : -375.0697 centred at (gu) : 90.19627 79.21730 94.79951 start vw surface at 0.1000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 166622 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20650 grid for indexing accessible points = 1.400000 m= 85401 mr = 122657 m= 30501 mr = 71189 m= 6980 mr = 24693 m= 1010 mr = 5265 m= 50 mr = 695 m= 0 mr = 15 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 2481 time to turn everything in is 0.9400000 number of dielectric boundary points 66050 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 19188 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) : 1.903268 object centre at (A) : 14.51600 3.433499 14.43950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7308230 -0.1896230 midg,1,midg; midg,igrid,midg 0.1528651 0.2912665 1,midg,midg; igrid,midg,midg 0.1172829 0.3701301 gauss-seidel spectral radius is 0.9992424 estimated iterations to convergence 287 setup time was (sec) 1.180000 now iterating at: 07:48:57 rms-change max change #iterations 9.627092 424.3824 at 10iterations 5.560429 137.6952 at 20iterations 3.196402 77.94225 at 30iterations 1.837602 43.28708 at 40iterations 1.053799 19.44617 at 50iterations 0.6040726 12.12471 at 60iterations 0.3452301 6.620163 at 70iterations 0.1977640 3.860100 at 80iterations 0.1129092 2.086960 at 90iterations 6.4629488E-02 1.183754 at 100iterations 3.6885571E-02 0.6943941 at 110iterations 2.1178693E-02 0.3889008 at 120iterations 1.2115501E-02 0.2220240 at 130iterations 6.9509773E-03 0.1352062 at 140iterations 4.0071402E-03 8.0305099E-02 at 150iterations 2.3350094E-03 4.5009613E-02 at 160iterations 1.3799540E-03 2.9014587E-02 at 170iterations 8.3697750E-04 1.5975952E-02 at 180iterations finished qdiffx linear iterations at : 07:49:08 total time elapsed so far: 12.36000 # loops : 180 mean,max change (kT/e) : 8.3697750E-04 1.5975952E-02 energy calculations done at 12.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.49000 DelPhi exited at 07:49:09 12.491u 0.248s 0:13.05 97.5% 0+0k 0+0io 0pf+0w