Tue Oct 11 07:11:17 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 Tue Oct 11 2011 at 07:11:17 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3514 !!! WARNING: HIR 51 has a net charge of 0.5140 !!! WARNING: HIR 147 has a net charge of 0.5140 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: 0.5948502 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): 0.5970000 50.87700 ymin,ymax (A): -8.425000 49.16000 zmin,zma (A): 1.198000 61.04500 x,y,z range (A): 50.28000 57.58500 59.84700 scale (grids/A): 0.5948502 object centre (A): 25.73700 20.36750 31.12150 number of atom coordinates read : 3514 total number of charged atoms : 3370 net assigned charge : 2.028007 assigned positive charge : 535.1431 centred at (gu) : 89.58490 89.96378 89.98708 assigned negative charge : -533.1168 centred at (gu) : 89.46851 89.87518 90.01011 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 8172 nv = 96 ne = 84 npr = 72760 no. pairs analyzed = 72760 no. exposed pairs = 3898 no. arc points = 26193 no. surface atoms = 1339 nbur = 2175 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 388 mr = 4905 m= 1 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 36 time to turn everything in is 0.3700000 number of dielectric boundary points 3618 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2799 ## 318 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 10416 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7486884E-09 -2.2176942E-10 midg,1,midg; midg,igrid,midg -3.0848408E-09 4.4692978E-09 1,midg,midg; igrid,midg,midg -4.7141846E-09 5.1480922E-09 gauss-seidel spectral radius is 0.9854419 estimated iterations to convergence 68 setup time was (sec) 0.5800000 now iterating at: 07:11:18 rms-change max change #iterations 0.1241964 16.36951 at 10iterations 1.0887344E-02 1.612324 at 20iterations 9.6083304E-04 0.1459846 at 30iterations 9.9726873E-05 1.2809753E-02 at 40iterations 1.3000651E-05 1.6498566E-03 at 50iterations finished qdiffx linear iterations at : 07:11:20 total time elapsed so far: 3.070000 # loops : 50 mean,max change (kT/e) : 1.3000651E-05 1.6498566E-03 energy calculations done at 3.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.270000 DelPhi exited at 07:11:21 3.277u 0.181s 0:03.93 87.7% 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 Tue Oct 11 2011 at 07:11:21 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3514 !!! WARNING: HIR 51 has a net charge of 0.5140 !!! WARNING: HIR 147 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.784551 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): 0.5970000 50.87700 ymin,ymax (A): -8.425000 49.16000 zmin,zma (A): 1.198000 61.04500 x,y,z range (A): 50.28000 57.58500 59.84700 scale (grids/A): 1.784551 object centre (A): 25.73700 20.36750 31.12150 number of atom coordinates read : 3514 total number of charged atoms : 3370 net assigned charge : 2.028007 assigned positive charge : 535.1431 centred at (gu) : 88.75375 89.89010 89.96008 assigned negative charge : -533.1168 centred at (gu) : 88.40531 89.62516 90.02994 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 89669 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26193 grid for indexing accessible points = 1.400000 m= 33200 mr = 65790 m= 4499 mr = 25607 m= 182 mr = 3046 m= 1 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 1284 time to turn everything in is 0.6100000 number of dielectric boundary points 33043 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 282 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 26282 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) : 0.5948502 object centre at (A) : 25.73700 20.36750 31.12150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.8652782E-03 -6.1069435E-04 midg,1,midg; midg,igrid,midg -9.7372029E-03 5.4114396E-03 1,midg,midg; igrid,midg,midg -1.3710588E-02 1.6848758E-02 gauss-seidel spectral radius is 0.9985290 estimated iterations to convergence 207 setup time was (sec) 0.8900000 now iterating at: 07:11:22 rms-change max change #iterations 4.479222 175.2597 at 10iterations 2.039096 72.65384 at 20iterations 0.9305060 28.76693 at 30iterations 0.4260464 13.44620 at 40iterations 0.1944177 5.985849 at 50iterations 8.8643178E-02 3.399351 at 60iterations 4.0447261E-02 1.195305 at 70iterations 1.8485084E-02 0.6324964 at 80iterations 8.4301969E-03 0.2680073 at 90iterations 3.8462733E-03 0.1080017 at 100iterations 1.7629139E-03 5.8477402E-02 at 110iterations 8.0555148E-04 2.4526596E-02 at 120iterations finished qdiffx linear iterations at : 07:11:28 total time elapsed so far: 7.270000 # loops : 120 mean,max change (kT/e) : 8.0555148E-04 2.4526596E-02 energy calculations done at 7.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.440000 DelPhi exited at 07:11:29 7.446u 0.193s 0:08.07 94.5% 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 07:11:29 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3514 !!! WARNING: HIR 51 has a net charge of 0.5140 !!! WARNING: HIR 147 has a net charge of 0.5140 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: 2.676826 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): 0.5970000 50.87700 ymin,ymax (A): -8.425000 49.16000 zmin,zma (A): 1.198000 61.04500 x,y,z range (A): 50.28000 57.58500 59.84700 scale (grids/A): 2.676826 object centre (A): 25.73700 20.36750 31.12150 number of atom coordinates read : 3514 total number of charged atoms : 3370 net assigned charge : 2.028007 assigned positive charge : 535.1431 centred at (gu) : 88.13031 89.83489 89.93996 assigned negative charge : -533.1168 centred at (gu) : 87.60796 89.43770 90.04459 start vw surface at 0.1700000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 207684 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26193 grid for indexing accessible points = 1.400000 m= 109495 mr = 158772 m= 38252 mr = 92444 m= 8051 mr = 31792 m= 930 mr = 6367 m= 36 mr = 682 m= 0 mr = 3 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 4504 time to turn everything in is 1.530000 number of dielectric boundary points 74388 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.670000 number of grid points assigned charge 26958 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) : 1.784551 object centre at (A) : 25.73700 20.36750 31.12150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1032645 -0.1104298 midg,1,midg; midg,igrid,midg -0.1651601 1.5515517E-02 1,midg,midg; igrid,midg,midg -0.1744137 0.1771494 gauss-seidel spectral radius is 0.9992416 estimated iterations to convergence 287 setup time was (sec) 1.840000 now iterating at: 07:11:31 rms-change max change #iterations 10.70167 284.9839 at 10iterations 6.165493 128.3226 at 20iterations 3.531653 62.37749 at 30iterations 2.021001 35.85150 at 40iterations 1.157483 23.78690 at 50iterations 0.6624839 10.91413 at 60iterations 0.3773682 6.271394 at 70iterations 0.2160636 3.657605 at 80iterations 0.1231765 2.111435 at 90iterations 7.0224978E-02 1.167353 at 100iterations 4.0136669E-02 0.7278478 at 110iterations 2.2898441E-02 0.3913956 at 120iterations 1.3054754E-02 0.2116508 at 130iterations 7.4491045E-03 0.1284494 at 140iterations 4.2610187E-03 8.3410263E-02 at 150iterations 2.4414889E-03 4.0561676E-02 at 160iterations 1.3975657E-03 2.4146080E-02 at 170iterations 8.0266956E-04 1.3807535E-02 at 180iterations finished qdiffx linear iterations at : 07:11:41 total time elapsed so far: 12.16000 # loops : 180 mean,max change (kT/e) : 8.0266956E-04 1.3807535E-02 energy calculations done at 12.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.34000 DelPhi exited at 07:11:42 12.344u 0.210s 0:12.85 97.6% 0+0k 0+0io 0pf+0w