Tue Oct 11 08:07:53 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 08:07:53 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2344 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6405643 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): -22.44300 29.51400 ymin,ymax (A): 21.45000 77.02600 zmin,zma (A): 2.645000 52.33900 x,y,z range (A): 51.95700 55.57600 49.69400 scale (grids/A): 0.6405643 object centre (A): 3.535501 49.23800 27.49200 number of atom coordinates read : 2344 total number of charged atoms : 2206 net assigned charge : 4.500012 assigned positive charge : 353.1133 centred at (gu) : 89.98519 87.81612 91.96342 assigned negative charge : -348.6138 centred at (gu) : 89.77666 87.87716 91.91182 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6604 nv = 96 ne = 84 npr = 46942 no. pairs analyzed = 46942 no. exposed pairs = 3023 no. arc points = 21824 no. surface atoms = 1009 nbur = 1335 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 358 mr = 3525 m= 1 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 19 time to turn everything in is 0.1700000 number of dielectric boundary points 3396 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2116 ## 196 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7713 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.7571809E-10 1.7900259E-08 midg,1,midg; midg,igrid,midg 2.0367711E-08 2.6580044E-11 1,midg,midg; igrid,midg,midg -1.6194315E-08 2.7752424E-08 gauss-seidel spectral radius is 0.9873559 estimated iterations to convergence 73 setup time was (sec) 0.3700000 now iterating at: 08:07:53 rms-change max change #iterations 0.1365211 22.26924 at 10iterations 1.3501431E-02 1.798264 at 20iterations 1.3728489E-03 0.1841373 at 30iterations 1.5544926E-04 2.6949883E-02 at 40iterations 3.2547643E-05 7.1249008E-03 at 50iterations finished qdiffx linear iterations at : 08:07:56 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 3.2547643E-05 7.1249008E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 08:07:57 3.401u 0.180s 0:03.94 90.8% 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 08:07:57 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2344 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: 1.921693 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): -22.44300 29.51400 ymin,ymax (A): 21.45000 77.02600 zmin,zma (A): 2.645000 52.33900 x,y,z range (A): 51.95700 55.57600 49.69400 scale (grids/A): 1.921693 object centre (A): 3.535501 49.23800 27.49200 number of atom coordinates read : 2344 total number of charged atoms : 2206 net assigned charge : 4.500012 assigned positive charge : 353.1133 centred at (gu) : 89.95499 83.44810 95.88976 assigned negative charge : -348.6138 centred at (gu) : 89.32990 83.63181 95.73533 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 70325 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21824 grid for indexing accessible points = 1.400000 m= 25763 mr = 47497 m= 4241 mr = 18936 m= 284 mr = 2607 m= 6 mr = 121 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 149 time to turn everything in is 0.3600000 number of dielectric boundary points 31458 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 125 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 17377 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) : 0.6405643 object centre at (A) : 3.535501 49.23800 27.49200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1313443E-03 3.3953965E-02 midg,1,midg; midg,igrid,midg 5.0886944E-02 2.5994832E-02 1,midg,midg; igrid,midg,midg -1.9465134E-02 3.3888478E-02 gauss-seidel spectral radius is 0.9986324 estimated iterations to convergence 214 setup time was (sec) 0.5800000 now iterating at: 08:07:57 rms-change max change #iterations 4.103741 162.5068 at 10iterations 1.909958 66.77265 at 20iterations 0.8915033 33.29040 at 30iterations 0.4183732 14.04649 at 40iterations 0.1947701 6.465519 at 50iterations 9.0931378E-02 3.255646 at 60iterations 4.2450283E-02 1.347885 at 70iterations 1.9894181E-02 0.6398420 at 80iterations 9.2796348E-03 0.2850475 at 90iterations 4.3878704E-03 0.1457748 at 100iterations 2.0575563E-03 6.8241596E-02 at 110iterations 9.8207826E-04 3.4550667E-02 at 120iterations finished qdiffx linear iterations at : 08:08:04 total time elapsed so far: 7.710000 # loops : 120 mean,max change (kT/e) : 9.8207826E-04 3.4550667E-02 energy calculations done at 7.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.850000 DelPhi exited at 08:08:05 7.849u 0.191s 0:08.32 96.5% 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 08:08:05 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2344 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: 2.882539 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): -22.44300 29.51400 ymin,ymax (A): 21.45000 77.02600 zmin,zma (A): 2.645000 52.33900 x,y,z range (A): 51.95700 55.57600 49.69400 scale (grids/A): 2.882539 object centre (A): 3.535501 49.23800 27.49200 number of atom coordinates read : 2344 total number of charged atoms : 2206 net assigned charge : 4.500012 assigned positive charge : 353.1133 centred at (gu) : 89.93253 80.17197 98.83451 assigned negative charge : -348.6138 centred at (gu) : 88.99471 80.44763 98.60295 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 162520 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21824 grid for indexing accessible points = 1.400000 m= 82057 mr = 115630 m= 30911 mr = 66462 m= 7549 mr = 25017 m= 1249 mr = 5561 m= 113 mr = 856 m= 3 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 498 time to turn everything in is 0.9200000 number of dielectric boundary points 70824 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 17647 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) : 1.921693 object centre at (A) : 3.535501 49.23800 27.49200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.9126086E-04 0.3375605 midg,1,midg; midg,igrid,midg 0.4761431 0.5349944 1,midg,midg; igrid,midg,midg -0.1698286 0.4800521 gauss-seidel spectral radius is 0.9992620 estimated iterations to convergence 291 setup time was (sec) 1.150000 now iterating at: 08:08:06 rms-change max change #iterations 9.708602 383.4373 at 10iterations 5.716561 141.1169 at 20iterations 3.349813 77.98779 at 30iterations 1.950838 40.14989 at 40iterations 1.133868 24.13106 at 50iterations 0.6567855 15.33348 at 60iterations 0.3803103 7.780095 at 70iterations 0.2198744 4.513893 at 80iterations 0.1271519 2.259024 at 90iterations 7.3236182E-02 1.345443 at 100iterations 4.2140681E-02 0.8016739 at 110iterations 2.4335353E-02 0.4590263 at 120iterations 1.4011256E-02 0.2661610 at 130iterations 8.0842376E-03 0.1600018 at 140iterations 4.6541286E-03 9.4080925E-02 at 150iterations 2.6834249E-03 4.8532486E-02 at 160iterations 1.5462248E-03 3.0796051E-02 at 170iterations 8.9493382E-04 1.5566587E-02 at 180iterations finished qdiffx linear iterations at : 08:08:18 total time elapsed so far: 12.53000 # loops : 180 mean,max change (kT/e) : 8.9493382E-04 1.5566587E-02 energy calculations done at 12.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.66000 DelPhi exited at 08:08:18 12.661u 0.214s 0:13.16 97.7% 0+0k 0+0io 0pf+0w