Sun Oct 9 07:39:45 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 Sun Oct 9 2011 at 07:39:46 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1688 !!! WARNING: NAP 164 has a net charge of -2.7230 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: 0.7330986 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): 4.356000 48.61000 ymin,ymax (A): 21.35900 69.92000 zmin,zma (A): -7.840000 35.87900 x,y,z range (A): 44.25400 48.56100 43.71900 scale (grids/A): 0.7330986 object centre (A): 26.48300 45.63950 14.01950 number of atom coordinates read : 1688 total number of charged atoms : 1551 net assigned charge : -12.22299 assigned positive charge : 249.5312 centred at (gu) : 90.67381 89.32446 89.38309 assigned negative charge : -261.7541 centred at (gu) : 90.68684 89.16261 89.74100 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6056 nv = 96 ne = 84 npr = 36648 no. pairs analyzed = 36648 no. exposed pairs = 2083 no. arc points = 14678 no. surface atoms = 707 nbur = 981 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 417 mr = 3403 m= 3 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 139 time to turn everything in is 0.2800000 number of dielectric boundary points 2993 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1134 ## 69 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 6459 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.3355075E-08 -4.0266167E-07 midg,1,midg; midg,igrid,midg -3.4467402E-07 -6.3217385E-08 1,midg,midg; igrid,midg,midg -1.5579539E-07 -2.2026491E-07 gauss-seidel spectral radius is 0.9902588 estimated iterations to convergence 82 setup time was (sec) 0.6500000 now iterating at: 07:39:47 rms-change max change #iterations 0.2143187 30.14191 at 10iterations 2.7902974E-02 3.944688 at 20iterations 3.7818239E-03 0.6213875 at 30iterations 4.8440072E-04 7.7692032E-02 at 40iterations 6.4709260E-05 8.5830688E-03 at 50iterations finished qdiffx linear iterations at : 07:39:50 total time elapsed so far: 4.180000 # loops : 50 mean,max change (kT/e) : 6.4709260E-05 8.5830688E-03 energy calculations done at 4.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.420000 DelPhi exited at 07:39:51 4.420u 0.432s 0:05.11 94.9% 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 Sun Oct 9 2011 at 07:39:51 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1688 !!! WARNING: NAP 164 has a net charge of -2.7230 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: 2.199296 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): 4.356000 48.61000 ymin,ymax (A): 21.35900 69.92000 zmin,zma (A): -7.840000 35.87900 x,y,z range (A): 44.25400 48.56100 43.71900 scale (grids/A): 2.199296 object centre (A): 26.48300 45.63950 14.01950 number of atom coordinates read : 1688 total number of charged atoms : 1551 net assigned charge : -12.22299 assigned positive charge : 249.5312 centred at (gu) : 92.02164 87.97354 88.14923 assigned negative charge : -261.7541 centred at (gu) : 92.06056 87.48798 89.22308 start vw surface at 0.1300000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 63790 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14678 grid for indexing accessible points = 1.400000 m= 25501 mr = 43893 m= 5183 mr = 19624 m= 475 mr = 3714 m= 17 mr = 220 m= 0 mr = 9 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 3345 time to turn everything in is 0.7000000 number of dielectric boundary points 27506 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 37 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 12365 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) : 0.7330986 object centre at (A) : 26.48300 45.63950 14.01950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3329854E-02 -9.1333747E-02 midg,1,midg; midg,igrid,midg -8.6561412E-02 2.6023432E-03 1,midg,midg; igrid,midg,midg -5.8358014E-02 -6.9290169E-02 gauss-seidel spectral radius is 0.9988631 estimated iterations to convergence 235 setup time was (sec) 1.030000 now iterating at: 07:39:52 rms-change max change #iterations 4.471195 201.3190 at 10iterations 2.236307 81.72404 at 20iterations 1.117579 39.03589 at 30iterations 0.5568497 19.14908 at 40iterations 0.2789782 9.023336 at 50iterations 0.1397955 4.433093 at 60iterations 6.9573417E-02 2.295809 at 70iterations 3.4754790E-02 1.136884 at 80iterations 1.7424056E-02 0.5242519 at 90iterations 8.7395282E-03 0.2911978 at 100iterations 4.3591512E-03 0.1429287 at 110iterations 2.1864932E-03 7.0251465E-02 at 120iterations finished qdiffx linear iterations at : 07:40:01 total time elapsed so far: 9.920000 # loops : 120 mean,max change (kT/e) : 2.1864932E-03 7.0251465E-02 energy calculations done at 9.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.13000 DelPhi exited at 07:40:02 10.136u 0.465s 0:10.89 97.2% 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 Sun Oct 9 2011 at 07:40:02 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1688 !!! WARNING: NAP 164 has a net charge of -2.7230 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: 3.298944 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): 4.356000 48.61000 ymin,ymax (A): 21.35900 69.92000 zmin,zma (A): -7.840000 35.87900 x,y,z range (A): 44.25400 48.56100 43.71900 scale (grids/A): 3.298944 object centre (A): 26.48300 45.63950 14.01950 number of atom coordinates read : 1688 total number of charged atoms : 1551 net assigned charge : -12.22299 assigned positive charge : 249.5312 centred at (gu) : 93.03243 86.96040 87.22398 assigned negative charge : -261.7541 centred at (gu) : 93.09082 86.23190 88.83475 start vw surface at 0.1200000 fill in re-entrant regions at 0.9100000 boundary points on vw surface= 146755 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14678 grid for indexing accessible points = 1.400000 m= 78309 mr = 105658 m= 33421 mr = 65287 m= 10003 mr = 28176 m= 1938 mr = 8128 m= 208 mr = 1359 m= 32 mr = 137 m= 3 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 1.080000 no. cavity mid-points inaccessible to solvent = 11173 time to turn everything in is 2.120000 number of dielectric boundary points 61904 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.260000 number of grid points assigned charge 12408 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) : 2.199296 object centre at (A) : 26.48300 45.63950 14.01950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3127950 -0.6339881 midg,1,midg; midg,igrid,midg -0.7243370 9.6657291E-02 1,midg,midg; igrid,midg,midg -0.3898197 -0.5634987 gauss-seidel spectral radius is 0.9992974 estimated iterations to convergence 298 setup time was (sec) 2.460000 now iterating at: 07:40:05 rms-change max change #iterations 9.802828 351.1832 at 10iterations 5.705169 139.1085 at 20iterations 3.318115 64.56888 at 30iterations 1.931118 41.08812 at 40iterations 1.125338 21.14513 at 50iterations 0.6531699 12.41681 at 60iterations 0.3804766 7.716971 at 70iterations 0.2212763 3.962693 at 80iterations 0.1289294 2.186038 at 90iterations 7.4908830E-02 1.373029 at 100iterations 4.3541666E-02 0.8208122 at 110iterations 2.5303623E-02 0.4357719 at 120iterations 1.4739696E-02 0.3088512 at 130iterations 8.5866172E-03 0.1564579 at 140iterations 5.0047422E-03 9.6475124E-02 at 150iterations 2.9159051E-03 5.2210808E-02 at 160iterations 1.6965745E-03 3.2315016E-02 at 170iterations 9.8676363E-04 1.8157959E-02 at 180iterations finished qdiffx linear iterations at : 07:40:20 total time elapsed so far: 17.36000 # loops : 180 mean,max change (kT/e) : 9.8676363E-04 1.8157959E-02 energy calculations done at 17.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.58000 DelPhi exited at 07:40:20 17.589u 0.569s 0:18.53 97.8% 0+0k 0+0io 0pf+0w