Tue Oct 11 04:22:42 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 04:22:42 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2760 !!! WARNING: HIR 71 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 0.6748304 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): -14.96100 32.88100 ymin,ymax (A): 7.004000 55.43700 zmin,zma (A): 25.32400 78.07800 x,y,z range (A): 47.84200 48.43300 52.75399 scale (grids/A): 0.6748304 object centre (A): 8.960001 31.22050 51.70100 number of atom coordinates read : 2760 total number of charged atoms : 2608 net assigned charge : 3.154016 assigned positive charge : 418.7877 centred at (gu) : 90.33527 90.46189 88.82095 assigned negative charge : -415.6343 centred at (gu) : 90.66190 90.28734 88.77341 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8436 nv = 96 ne = 84 npr = 56757 no. pairs analyzed = 56757 no. exposed pairs = 3386 no. arc points = 23570 no. surface atoms = 1133 nbur = 1627 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 490 mr = 4789 m= 4 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 60 time to turn everything in is 0.3400000 number of dielectric boundary points 4068 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2237 ## 207 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9792 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.1199945E-09 2.1208594E-08 midg,1,midg; midg,igrid,midg -3.8224222E-08 7.1473977E-08 1,midg,midg; igrid,midg,midg 1.0195406E-07 -9.7980163E-08 gauss-seidel spectral radius is 0.9886277 estimated iterations to convergence 76 setup time was (sec) 0.5600000 now iterating at: 04:22:43 rms-change max change #iterations 0.1855974 26.39666 at 10iterations 2.1018559E-02 2.923027 at 20iterations 2.3846666E-03 0.3014603 at 30iterations 2.8682436E-04 3.6145210E-02 at 40iterations 4.0348306E-05 5.2719116E-03 at 50iterations finished qdiffx linear iterations at : 04:22:45 total time elapsed so far: 3.040000 # loops : 50 mean,max change (kT/e) : 4.0348306E-05 5.2719116E-03 energy calculations done at 3.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.210000 DelPhi exited at 04:22:46 3.217u 0.154s 0:03.72 90.3% 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 04:22:46 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2760 !!! WARNING: HIR 71 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.024491 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): -14.96100 32.88100 ymin,ymax (A): 7.004000 55.43700 zmin,zma (A): 25.32400 78.07800 x,y,z range (A): 47.84200 48.43300 52.75399 scale (grids/A): 2.024491 object centre (A): 8.960001 31.22050 51.70100 number of atom coordinates read : 2760 total number of charged atoms : 2608 net assigned charge : 3.154016 assigned positive charge : 418.7877 centred at (gu) : 91.00506 91.38509 86.46234 assigned negative charge : -415.6343 centred at (gu) : 91.98551 90.86160 86.31987 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 90486 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23570 grid for indexing accessible points = 1.400000 m= 34764 mr = 64284 m= 6019 mr = 26181 m= 395 mr = 3909 m= 4 mr = 149 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1624 time to turn everything in is 0.6400000 number of dielectric boundary points 37145 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 111 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 20626 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) : 0.6748304 object centre at (A) : 8.960001 31.22050 51.70100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0702851E-02 1.0228798E-02 midg,1,midg; midg,igrid,midg -1.6294356E-02 4.8558231E-02 1,midg,midg; igrid,midg,midg 8.8503912E-02 -3.1917401E-02 gauss-seidel spectral radius is 0.9987987 estimated iterations to convergence 228 setup time was (sec) 0.9200000 now iterating at: 04:22:47 rms-change max change #iterations 5.001834 193.9772 at 10iterations 2.456813 72.92352 at 20iterations 1.204505 38.57117 at 30iterations 0.5945368 17.99450 at 40iterations 0.2913667 8.377542 at 50iterations 0.1437095 4.053817 at 60iterations 7.0523947E-02 2.193599 at 70iterations 3.4767397E-02 1.150253 at 80iterations 1.7052637E-02 0.4944115 at 90iterations 8.3927214E-03 0.2456799 at 100iterations 4.1294452E-03 0.1165276 at 110iterations 2.0284837E-03 6.2480927E-02 at 120iterations finished qdiffx linear iterations at : 04:22:54 total time elapsed so far: 7.360000 # loops : 120 mean,max change (kT/e) : 2.0284837E-03 6.2480927E-02 energy calculations done at 7.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.540000 DelPhi exited at 04:22:54 7.541u 0.186s 0:08.14 94.8% 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 Tue Oct 11 2011 at 04:22:54 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2760 !!! WARNING: HIR 71 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 3.036737 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): -14.96100 32.88100 ymin,ymax (A): 7.004000 55.43700 zmin,zma (A): 25.32400 78.07800 x,y,z range (A): 47.84200 48.43300 52.75399 scale (grids/A): 3.036737 object centre (A): 8.960001 31.22050 51.70100 number of atom coordinates read : 2760 total number of charged atoms : 2608 net assigned charge : 3.154016 assigned positive charge : 418.7877 centred at (gu) : 91.50748 92.07743 84.69334 assigned negative charge : -415.6343 centred at (gu) : 92.97803 91.29240 84.47968 start vw surface at 0.1500000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 209104 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23570 grid for indexing accessible points = 1.400000 m= 110455 mr = 154902 m= 42442 mr = 91787 m= 11038 mr = 34684 m= 1830 mr = 8522 m= 141 mr = 1284 m= 2 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 5310 time to turn everything in is 1.630000 number of dielectric boundary points 83771 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 20862 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) : 2.024491 object centre at (A) : 8.960001 31.22050 51.70100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1439362 1.4496790E-02 midg,1,midg; midg,igrid,midg -0.1536116 0.5428401 1,midg,midg; igrid,midg,midg 0.7163495 -0.1718463 gauss-seidel spectral radius is 0.9992983 estimated iterations to convergence 298 setup time was (sec) 1.930000 now iterating at: 04:22:56 rms-change max change #iterations 11.36879 567.9341 at 10iterations 6.723588 133.1461 at 20iterations 3.974910 79.71665 at 30iterations 2.342094 45.73849 at 40iterations 1.378760 25.98590 at 50iterations 0.8111038 14.22967 at 60iterations 0.4764358 8.310268 at 70iterations 0.2799418 5.069094 at 80iterations 0.1638304 2.760109 at 90iterations 9.6107334E-02 1.664400 at 100iterations 5.6209806E-02 1.007832 at 110iterations 3.2900687E-02 0.5290394 at 120iterations 1.9290712E-02 0.3518982 at 130iterations 1.1268512E-02 0.1927633 at 140iterations 6.6287154E-03 0.1158409 at 150iterations 3.8949992E-03 6.6627502E-02 at 160iterations 2.3092940E-03 4.1717529E-02 at 170iterations 1.3785289E-03 2.2899628E-02 at 180iterations finished qdiffx linear iterations at : 04:23:06 total time elapsed so far: 12.06000 # loops : 180 mean,max change (kT/e) : 1.3785289E-03 2.2899628E-02 energy calculations done at 12.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.23000 DelPhi exited at 04:23:07 12.233u 0.245s 0:13.01 95.8% 0+0k 0+0io 0pf+0w