Mon Oct 10 13:58:49 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 Mon Oct 10 2011 at 13:58:49 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4244 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: 0.5848145 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): -25.79100 35.08300 ymin,ymax (A): 34.85500 92.30099 zmin,zma (A): 30.66900 89.29600 x,y,z range (A): 60.87400 57.44599 58.62700 scale (grids/A): 0.5848145 object centre (A): 4.646000 63.57800 59.98250 number of atom coordinates read : 4244 total number of charged atoms : 4108 net assigned charge : -0.9999584 assigned positive charge : 638.9243 centred at (gu) : 91.20883 89.56297 88.65531 assigned negative charge : -639.9275 centred at (gu) : 91.05410 89.69319 88.84426 start vw surface at 0.2100000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 9168 nv = 96 ne = 84 npr = 89933 no. pairs analyzed = 89933 no. exposed pairs = 4696 no. arc points = 31647 no. surface atoms = 1609 nbur = 2635 mkacc time = 0.2500000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 401 mr = 5392 m= 1 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 221 time to turn everything in is 0.5200000 number of dielectric boundary points 4136 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3275 ## 372 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 12128 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.8179446E-09 -5.5486500E-09 midg,1,midg; midg,igrid,midg 4.7716715E-09 -4.8242019E-09 1,midg,midg; igrid,midg,midg -4.7339261E-09 6.9116752E-09 gauss-seidel spectral radius is 0.9849927 estimated iterations to convergence 67 setup time was (sec) 0.7900000 now iterating at: 13:58:50 rms-change max change #iterations 0.1248140 16.19167 at 10iterations 1.0270151E-02 1.339499 at 20iterations 9.5462374E-04 0.1218519 at 30iterations 1.5591540E-04 2.1221161E-02 at 40iterations 4.4676337E-05 6.5728426E-03 at 50iterations finished qdiffx linear iterations at : 13:58:53 total time elapsed so far: 4.070000 # loops : 50 mean,max change (kT/e) : 4.4676337E-05 6.5728426E-03 energy calculations done at 4.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.230000 DelPhi exited at 13:58:54 4.229u 0.263s 0:04.99 89.7% 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 13:58:54 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4244 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: 1.754444 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): -25.79100 35.08300 ymin,ymax (A): 34.85500 92.30099 zmin,zma (A): 30.66900 89.29600 x,y,z range (A): 60.87400 57.44599 58.62700 scale (grids/A): 1.754444 object centre (A): 4.646000 63.57800 59.98250 number of atom coordinates read : 4244 total number of charged atoms : 4108 net assigned charge : -0.9999584 assigned positive charge : 638.9243 centred at (gu) : 93.62515 88.68770 85.96471 assigned negative charge : -639.9275 centred at (gu) : 93.16177 89.07918 86.53222 start vw surface at 0.2000000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 102384 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31647 grid for indexing accessible points = 1.400000 m= 35207 mr = 74860 m= 4795 mr = 26324 m= 180 mr = 3021 m= 2 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 7468 time to turn everything in is 0.8800000 number of dielectric boundary points 38304 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 288 ## 1 charges are in solution ## iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 31962 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) : 0.5848145 object centre at (A) : 4.646000 63.57800 59.98250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4077722E-02 -3.3937734E-02 midg,1,midg; midg,igrid,midg 2.5044026E-02 -2.9506341E-02 1,midg,midg; igrid,midg,midg -1.1080476E-02 4.7252949E-02 gauss-seidel spectral radius is 0.9985363 estimated iterations to convergence 207 setup time was (sec) 1.180000 now iterating at: 13:58:55 rms-change max change #iterations 4.801787 170.0586 at 10iterations 2.185494 68.70728 at 20iterations 0.9956239 30.65926 at 30iterations 0.4539905 13.18560 at 40iterations 0.2082931 5.778374 at 50iterations 9.5112048E-02 2.517968 at 60iterations 4.3514896E-02 1.158798 at 70iterations 1.9914536E-02 0.5840950 at 80iterations 9.1091385E-03 0.2564487 at 90iterations 4.1811257E-03 0.1159191 at 100iterations 1.9252911E-03 5.5292130E-02 at 110iterations 8.9447777E-04 2.6378632E-02 at 120iterations finished qdiffx linear iterations at : 13:59:03 total time elapsed so far: 9.640000 # loops : 120 mean,max change (kT/e) : 8.9447777E-04 2.6378632E-02 energy calculations done at 9.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.810000 DelPhi exited at 13:59:04 9.808u 0.306s 0:10.43 96.8% 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 13:59:04 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4244 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: 2.631665 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): -25.79100 35.08300 ymin,ymax (A): 34.85500 92.30099 zmin,zma (A): 30.66900 89.29600 x,y,z range (A): 60.87400 57.44599 58.62700 scale (grids/A): 2.631665 object centre (A): 4.646000 63.57800 59.98250 number of atom coordinates read : 4244 total number of charged atoms : 4108 net assigned charge : -0.9999584 assigned positive charge : 638.9243 centred at (gu) : 95.43746 88.03127 83.94675 assigned negative charge : -639.9275 centred at (gu) : 94.74253 88.61871 84.79830 start vw surface at 0.2000000 fill in re-entrant regions at 0.7400000 boundary points on vw surface= 238016 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31647 grid for indexing accessible points = 1.400000 m= 118561 mr = 181396 m= 38742 mr = 98305 m= 8318 mr = 31430 m= 900 mr = 6454 m= 32 mr = 561 m= 0 mr = 6 time to grow re-entrant surface = 1.350000 no. cavity mid-points inaccessible to solvent = 24476 time to turn everything in is 2.230000 number of dielectric boundary points 86417 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 2.390000 number of grid points assigned charge 32850 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) : 1.754444 object centre at (A) : 4.646000 63.57800 59.98250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8504097 -0.4126479 midg,1,midg; midg,igrid,midg 0.3238399 -0.3262396 1,midg,midg; igrid,midg,midg -7.9241201E-02 0.3829814 gauss-seidel spectral radius is 0.9992546 estimated iterations to convergence 289 setup time was (sec) 2.560000 now iterating at: 13:59:07 rms-change max change #iterations 11.63583 344.9938 at 10iterations 6.805212 141.2991 at 20iterations 3.953049 72.44688 at 30iterations 2.289370 43.16475 at 40iterations 1.321768 24.49515 at 50iterations 0.7629545 13.69373 at 60iterations 0.4390397 8.290609 at 70iterations 0.2528429 4.170704 at 80iterations 0.1455869 2.291892 at 90iterations 8.3837591E-02 1.321428 at 100iterations 4.8116799E-02 0.7864070 at 110iterations 2.7664032E-02 0.4590998 at 120iterations 1.5922869E-02 0.2402115 at 130iterations 9.1516813E-03 0.1437740 at 140iterations 5.2740686E-03 8.2983017E-02 at 150iterations 3.0458982E-03 5.1145554E-02 at 160iterations 1.7638460E-03 2.9286385E-02 at 170iterations 1.0305223E-03 1.7284870E-02 at 180iterations finished qdiffx linear iterations at : 13:59:21 total time elapsed so far: 16.67000 # loops : 180 mean,max change (kT/e) : 1.0305223E-03 1.7284870E-02 energy calculations done at 16.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.86000 DelPhi exited at 13:59:23 16.858u 0.313s 0:18.63 92.1% 0+0k 0+0io 0pf+0w