Mon Oct 10 19:41:53 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 19:41:53 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2736 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: GLM 268 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6421820 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): 13.65100 62.65700 ymin,ymax (A): -18.26400 37.17200 zmin,zma (A): 31.22700 84.59900 x,y,z range (A): 49.00600 55.43600 53.37200 scale (grids/A): 0.6421820 object centre (A): 38.15400 9.454000 57.91300 number of atom coordinates read : 2736 total number of charged atoms : 2593 net assigned charge : 6.420031 assigned positive charge : 411.2055 centred at (gu) : 91.61652 92.96794 89.62984 assigned negative charge : -404.7865 centred at (gu) : 91.59581 93.05803 89.55527 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7525 nv = 96 ne = 84 npr = 55928 no. pairs analyzed = 55928 no. exposed pairs = 3447 no. arc points = 24675 no. surface atoms = 1156 nbur = 1580 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 434 mr = 4028 m= 4 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3873 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2454 ## 251 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 9080 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.4113798E-10 1.8145551E-08 midg,1,midg; midg,igrid,midg 1.1618264E-08 -3.3418095E-09 1,midg,midg; igrid,midg,midg 5.4699254E-09 1.8038676E-08 gauss-seidel spectral radius is 0.9874516 estimated iterations to convergence 73 setup time was (sec) 0.4200000 now iterating at: 19:41:54 rms-change max change #iterations 0.1510516 23.26194 at 10iterations 1.4952714E-02 2.225101 at 20iterations 1.4757680E-03 0.2019844 at 30iterations 1.4838077E-04 1.9264221E-02 at 40iterations 1.5017699E-05 2.0799637E-03 at 50iterations finished qdiffx linear iterations at : 19:41:56 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 1.5017699E-05 2.0799637E-03 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 19:41:57 3.428u 0.147s 0:04.24 83.9% 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 Mon Oct 10 2011 at 19:41:57 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2736 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: GLM 268 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.926546 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): 13.65100 62.65700 ymin,ymax (A): -18.26400 37.17200 zmin,zma (A): 31.22700 84.59900 x,y,z range (A): 49.00600 55.43600 53.37200 scale (grids/A): 1.926546 object centre (A): 38.15400 9.454000 57.91300 number of atom coordinates read : 2736 total number of charged atoms : 2593 net assigned charge : 6.420031 assigned positive charge : 411.2055 centred at (gu) : 94.84905 98.90316 88.88870 assigned negative charge : -404.7865 centred at (gu) : 94.78743 99.17383 88.66555 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 80678 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24675 grid for indexing accessible points = 1.400000 m= 28828 mr = 55059 m= 5121 mr = 20770 m= 354 mr = 3179 m= 6 mr = 149 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 349 time to turn everything in is 0.4000000 number of dielectric boundary points 35830 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 149 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 20395 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) : 0.6421820 object centre at (A) : 38.15400 9.454000 57.91300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.6044252E-03 3.5737444E-02 midg,1,midg; midg,igrid,midg 5.1216795E-03 2.8871948E-02 1,midg,midg; igrid,midg,midg 1.2376628E-02 1.9054541E-02 gauss-seidel spectral radius is 0.9986797 estimated iterations to convergence 218 setup time was (sec) 0.6100000 now iterating at: 19:41:58 rms-change max change #iterations 4.471281 192.3916 at 10iterations 2.116752 81.98783 at 20iterations 0.9964089 29.01548 at 30iterations 0.4727300 14.68185 at 40iterations 0.2241941 8.087780 at 50iterations 0.1062392 3.361704 at 60iterations 5.0176550E-02 1.624932 at 70iterations 2.3840515E-02 0.6964273 at 80iterations 1.1312353E-02 0.3467941 at 90iterations 5.3545283E-03 0.1640129 at 100iterations 2.5433369E-03 7.8070641E-02 at 110iterations 1.2066806E-03 3.5254478E-02 at 120iterations finished qdiffx linear iterations at : 19:42:05 total time elapsed so far: 7.710000 # loops : 120 mean,max change (kT/e) : 1.2066806E-03 3.5254478E-02 energy calculations done at 7.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.840000 DelPhi exited at 19:42:06 7.846u 0.229s 0:08.47 95.1% 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 19:42:06 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2736 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: GLM 268 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.889819 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): 13.65100 62.65700 ymin,ymax (A): -18.26400 37.17200 zmin,zma (A): 31.22700 84.59900 x,y,z range (A): 49.00600 55.43600 53.37200 scale (grids/A): 2.889819 object centre (A): 38.15400 9.454000 57.91300 number of atom coordinates read : 2736 total number of charged atoms : 2593 net assigned charge : 6.420031 assigned positive charge : 411.2055 centred at (gu) : 97.27326 103.3543 88.33289 assigned negative charge : -404.7865 centred at (gu) : 97.18105 103.7606 87.99830 start vw surface at 0.1000000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 186916 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24675 grid for indexing accessible points = 1.400000 m= 92251 mr = 133844 m= 34452 mr = 74448 m= 9195 mr = 27261 m= 1544 mr = 6898 m= 113 mr = 1107 m= 4 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.6300001 no. cavity mid-points inaccessible to solvent = 1255 time to turn everything in is 1.110000 number of dielectric boundary points 80862 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 20743 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) : 1.926546 object centre at (A) : 38.15400 9.454000 57.91300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7114924E-02 0.2769079 midg,1,midg; midg,igrid,midg 9.6060738E-02 0.3564981 1,midg,midg; igrid,midg,midg 0.2200026 0.2129743 gauss-seidel spectral radius is 0.9992736 estimated iterations to convergence 293 setup time was (sec) 1.390000 now iterating at: 19:42:07 rms-change max change #iterations 10.37674 387.2455 at 10iterations 6.082293 133.4404 at 20iterations 3.538658 67.29196 at 30iterations 2.055928 36.91463 at 40iterations 1.196103 19.75904 at 50iterations 0.6920040 13.78155 at 60iterations 0.4018870 7.619789 at 70iterations 0.2322707 4.298176 at 80iterations 0.1343139 2.387693 at 90iterations 7.7826887E-02 1.379805 at 100iterations 4.5012906E-02 0.7950134 at 110iterations 2.5994094E-02 0.4693731 at 120iterations 1.5012561E-02 0.2571745 at 130iterations 8.6693726E-03 0.1405258 at 140iterations 5.0116330E-03 8.8562012E-02 at 150iterations 2.9023145E-03 5.1235199E-02 at 160iterations 1.6775569E-03 2.9218674E-02 at 170iterations 9.7395206E-04 1.7683029E-02 at 180iterations finished qdiffx linear iterations at : 19:42:20 total time elapsed so far: 14.37000 # loops : 180 mean,max change (kT/e) : 9.7395206E-04 1.7683029E-02 energy calculations done at 14.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.50000 DelPhi exited at 19:42:21 14.501u 0.269s 0:15.16 97.3% 0+0k 0+0io 0pf+0w