Mon Oct 10 20:31:19 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 20:31:19 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3316 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5961851 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): -34.15700 22.59300 ymin,ymax (A): -4.291000 55.42200 zmin,zma (A): -8.064000 45.79300 x,y,z range (A): 56.75000 59.71300 53.85700 scale (grids/A): 0.5961851 object centre (A): -5.781999 25.56550 18.86450 number of atom coordinates read : 3316 total number of charged atoms : 3178 net assigned charge : 9.000004 assigned positive charge : 497.0953 centred at (gu) : 90.95907 87.98632 88.84614 assigned negative charge : -488.0970 centred at (gu) : 90.99468 87.79195 88.82436 start vw surface at 0.2400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 8057 nv = 96 ne = 84 npr = 63522 no. pairs analyzed = 63522 no. exposed pairs = 4751 no. arc points = 34202 no. surface atoms = 1564 nbur = 1752 mkacc time = 0.1900000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 438 mr = 3841 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.4700000 number of dielectric boundary points 4614 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3443 ## 331 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 9963 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.4896350E-09 3.4585272E-09 midg,1,midg; midg,igrid,midg -7.2740165E-09 7.1479653E-09 1,midg,midg; igrid,midg,midg 4.0555315E-09 2.6384750E-09 gauss-seidel spectral radius is 0.9855199 estimated iterations to convergence 68 setup time was (sec) 0.7700000 now iterating at: 20:31:20 rms-change max change #iterations 0.1155559 26.13290 at 10iterations 9.6410159E-03 1.346704 at 20iterations 8.3494536E-04 0.1167479 at 30iterations 7.9736114E-05 1.0600090E-02 at 40iterations 9.8608962E-06 1.3041496E-03 at 50iterations finished qdiffx linear iterations at : 20:31:23 total time elapsed so far: 4.040000 # loops : 50 mean,max change (kT/e) : 9.8608962E-06 1.3041496E-03 energy calculations done at 4.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.280000 DelPhi exited at 20:31:24 4.280u 0.187s 0:05.20 85.7% 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 20:31:25 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3316 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.788555 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): -34.15700 22.59300 ymin,ymax (A): -4.291000 55.42200 zmin,zma (A): -8.064000 45.79300 x,y,z range (A): 56.75000 59.71300 53.85700 scale (grids/A): 1.788555 object centre (A): -5.781999 25.56550 18.86450 number of atom coordinates read : 3316 total number of charged atoms : 3178 net assigned charge : 9.000004 assigned positive charge : 497.0953 centred at (gu) : 92.87624 83.95814 86.53745 assigned negative charge : -488.0970 centred at (gu) : 92.98378 83.37523 86.47297 start vw surface at 0.2300000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 85830 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34202 grid for indexing accessible points = 1.400000 m= 29431 mr = 54759 m= 4562 mr = 19991 m= 231 mr = 2563 m= 7 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 1879 time to turn everything in is 0.8100000 number of dielectric boundary points 42700 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 236 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 24749 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) : 0.5961851 object centre at (A) : -5.781999 25.56550 18.86450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.2703728E-03 2.2675332E-03 midg,1,midg; midg,igrid,midg 3.7379637E-02 6.4337105E-02 1,midg,midg; igrid,midg,midg -8.9106141E-03 3.4719303E-02 gauss-seidel spectral radius is 0.9985566 estimated iterations to convergence 209 setup time was (sec) 1.180000 now iterating at: 20:31:26 rms-change max change #iterations 4.280524 177.4870 at 10iterations 1.947260 63.11503 at 20iterations 0.8859436 31.78450 at 30iterations 0.4052990 12.21590 at 40iterations 0.1859188 5.852286 at 50iterations 8.4404260E-02 2.853465 at 60iterations 3.8691822E-02 1.166304 at 70iterations 1.7796965E-02 0.5088844 at 80iterations 8.1298659E-03 0.2506075 at 90iterations 3.7220807E-03 0.1160736 at 100iterations 1.7032636E-03 5.4515839E-02 at 110iterations 7.8031898E-04 2.3653984E-02 at 120iterations finished qdiffx linear iterations at : 20:31:35 total time elapsed so far: 9.620000 # loops : 120 mean,max change (kT/e) : 7.8031898E-04 2.3653984E-02 energy calculations done at 9.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.860000 DelPhi exited at 20:31:35 9.860u 0.251s 0:10.55 95.8% 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 20:31:35 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3316 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.682833 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): -34.15700 22.59300 ymin,ymax (A): -4.291000 55.42200 zmin,zma (A): -8.064000 45.79300 x,y,z range (A): 56.75000 59.71300 53.85700 scale (grids/A): 2.682833 object centre (A): -5.781999 25.56550 18.86450 number of atom coordinates read : 3316 total number of charged atoms : 3178 net assigned charge : 9.000004 assigned positive charge : 497.0953 centred at (gu) : 94.31409 80.93707 84.80598 assigned negative charge : -488.0970 centred at (gu) : 94.47569 80.06268 84.70938 start vw surface at 0.2000000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 198099 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34202 grid for indexing accessible points = 1.400000 m= 94511 mr = 134465 m= 33391 mr = 72801 m= 7948 mr = 25364 m= 936 mr = 5608 m= 33 mr = 490 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 1.190000 no. cavity mid-points inaccessible to solvent = 6245 time to turn everything in is 1.990000 number of dielectric boundary points 96186 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 2.170000 number of grid points assigned charge 25422 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) : 1.788555 object centre at (A) : -5.781999 25.56550 18.86450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.8340878E-02 8.7532941E-03 midg,1,midg; midg,igrid,midg 0.5877697 0.9900925 1,midg,midg; igrid,midg,midg -0.1325689 0.4408043 gauss-seidel spectral radius is 0.9992731 estimated iterations to convergence 293 setup time was (sec) 2.380000 now iterating at: 20:31:38 rms-change max change #iterations 10.61604 325.9365 at 10iterations 6.362194 137.7045 at 20iterations 3.776346 74.87764 at 30iterations 2.221193 42.84240 at 40iterations 1.300533 26.43649 at 50iterations 0.7595068 14.60712 at 60iterations 0.4430439 8.642034 at 70iterations 0.2574977 4.663937 at 80iterations 0.1496409 2.627823 at 90iterations 8.6649597E-02 1.595852 at 100iterations 5.0218251E-02 0.8713989 at 110iterations 2.9064978E-02 0.5326538 at 120iterations 1.6847685E-02 0.3056288 at 130iterations 9.7305579E-03 0.1727200 at 140iterations 5.6277034E-03 0.1030312 at 150iterations 3.2579373E-03 6.3543320E-02 at 160iterations 1.8802371E-03 3.3344269E-02 at 170iterations 1.0861449E-03 1.9946575E-02 at 180iterations finished qdiffx linear iterations at : 20:31:51 total time elapsed so far: 15.87000 # loops : 180 mean,max change (kT/e) : 1.0861449E-03 1.9946575E-02 energy calculations done at 15.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.10000 DelPhi exited at 20:31:52 16.105u 0.254s 0:16.67 98.0% 0+0k 0+0io 0pf+0w