Mon Oct 10 18:48:53 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 Mon Oct 10 2011 at 18:48:53 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2453 !!! WARNING: HIR 86 has a net charge of 0.5140 !!! WARNING: HIR 257 has a net charge of 0.5140 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: 0.6025525 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): -91.37200 -39.13500 ymin,ymax (A): 57.45300 116.5350 zmin,zma (A): 65.77000 107.7810 x,y,z range (A): 52.23700 59.08199 42.01100 scale (grids/A): 0.6025525 object centre (A): -65.25350 86.99400 86.77550 number of atom coordinates read : 2453 total number of charged atoms : 2314 net assigned charge : -0.9719902 assigned positive charge : 372.7217 centred at (gu) : 89.60371 87.62798 90.76887 assigned negative charge : -373.6945 centred at (gu) : 89.54391 87.64622 90.90907 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5853 nv = 96 ne = 84 npr = 50061 no. pairs analyzed = 50061 no. exposed pairs = 2967 no. arc points = 20665 no. surface atoms = 995 nbur = 1458 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 283 mr = 3272 m= 0 mr = 23 time to grow re-entrant surface = 9.0000011E-02 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.2000000 number of dielectric boundary points 2841 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2023 ## 225 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7286 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.0194235E-09 -6.9049193E-09 midg,1,midg; midg,igrid,midg 5.0904392E-10 -6.4719446E-10 1,midg,midg; igrid,midg,midg -2.9330907E-09 1.6719869E-09 gauss-seidel spectral radius is 0.9857274 estimated iterations to convergence 69 setup time was (sec) 0.4000000 now iterating at: 18:48:54 rms-change max change #iterations 0.1111886 16.89928 at 10iterations 9.7437110E-03 1.535493 at 20iterations 8.8009966E-04 0.1458054 at 30iterations 1.0159584E-04 1.9920349E-02 at 40iterations 1.5926566E-05 3.3497810E-03 at 50iterations finished qdiffx linear iterations at : 18:48:57 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 1.5926566E-05 3.3497810E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 18:48:57 3.420u 0.156s 0:03.87 92.2% 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 Mon Oct 10 2011 at 18:48:57 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2453 !!! WARNING: HIR 86 has a net charge of 0.5140 !!! WARNING: HIR 257 has a net charge of 0.5140 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: 1.807657 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): -91.37200 -39.13500 ymin,ymax (A): 57.45300 116.5350 zmin,zma (A): 65.77000 107.7810 x,y,z range (A): 52.23700 59.08199 42.01100 scale (grids/A): 1.807657 object centre (A): -65.25350 86.99400 86.77550 number of atom coordinates read : 2453 total number of charged atoms : 2314 net assigned charge : -0.9719902 assigned positive charge : 372.7217 centred at (gu) : 88.81036 82.88342 92.30611 assigned negative charge : -373.6945 centred at (gu) : 88.63151 82.93822 92.72697 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 63984 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20665 grid for indexing accessible points = 1.400000 m= 22432 mr = 44923 m= 3097 mr = 16516 m= 139 mr = 1874 m= 0 mr = 33 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 1521 time to turn everything in is 0.3300000 number of dielectric boundary points 26306 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 150 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 18078 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) : 0.6025525 object centre at (A) : -65.25350 86.99400 86.77550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.0106867E-03 -7.8512942E-03 midg,1,midg; midg,igrid,midg -2.6005359E-02 -8.9806132E-03 1,midg,midg; igrid,midg,midg -1.0977157E-02 1.9928638E-02 gauss-seidel spectral radius is 0.9984647 estimated iterations to convergence 202 setup time was (sec) 0.5400000 now iterating at: 18:48:58 rms-change max change #iterations 3.794683 205.2623 at 10iterations 1.695325 62.22612 at 20iterations 0.7581987 25.44410 at 30iterations 0.3391759 11.62594 at 40iterations 0.1511735 5.078663 at 50iterations 6.7761451E-02 2.676091 at 60iterations 3.0441415E-02 1.039865 at 70iterations 1.3636273E-02 0.4810586 at 80iterations 6.1133211E-03 0.2051573 at 90iterations 2.7495916E-03 9.4200134E-02 at 100iterations 1.2345592E-03 4.1687012E-02 at 110iterations 5.5881112E-04 2.0008087E-02 at 120iterations finished qdiffx linear iterations at : 18:49:05 total time elapsed so far: 7.570000 # loops : 120 mean,max change (kT/e) : 5.5881112E-04 2.0008087E-02 energy calculations done at 7.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.710000 DelPhi exited at 18:49:06 7.714u 0.197s 0:08.36 94.4% 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 18:49:06 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2453 !!! WARNING: HIR 86 has a net charge of 0.5140 !!! WARNING: HIR 257 has a net charge of 0.5140 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: 2.711486 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): -91.37200 -39.13500 ymin,ymax (A): 57.45300 116.5350 zmin,zma (A): 65.77000 107.7810 x,y,z range (A): 52.23700 59.08199 42.01100 scale (grids/A): 2.711486 object centre (A): -65.25350 86.99400 86.77550 number of atom coordinates read : 2453 total number of charged atoms : 2314 net assigned charge : -0.9719902 assigned positive charge : 372.7217 centred at (gu) : 88.21535 79.32493 93.45905 assigned negative charge : -373.6945 centred at (gu) : 87.94714 79.40726 94.09043 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 148672 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20665 grid for indexing accessible points = 1.400000 m= 73283 mr = 109391 m= 25445 mr = 59945 m= 5436 mr = 20375 m= 648 mr = 3985 m= 19 mr = 384 m= 0 mr = 0 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 5180 time to turn everything in is 0.8400000 number of dielectric boundary points 59423 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 18507 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) : 1.807657 object centre at (A) : -65.25350 86.99400 86.77550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.3071033E-02 -5.3599652E-02 midg,1,midg; midg,igrid,midg -0.3923184 0.1020632 1,midg,midg; igrid,midg,midg -0.1708674 0.3248907 gauss-seidel spectral radius is 0.9992052 estimated iterations to convergence 280 setup time was (sec) 1.060000 now iterating at: 18:49:07 rms-change max change #iterations 9.113350 276.3697 at 10iterations 5.219774 128.0350 at 20iterations 2.966391 66.53854 at 30iterations 1.679297 42.98385 at 40iterations 0.9500967 19.62228 at 50iterations 0.5360440 13.28479 at 60iterations 0.3030368 5.909500 at 70iterations 0.1703060 3.241371 at 80iterations 9.6140593E-02 2.215546 at 90iterations 5.4170426E-02 1.035404 at 100iterations 3.0378038E-02 0.6927509 at 110iterations 1.7093891E-02 0.3408813 at 120iterations 9.6444422E-03 0.1817932 at 130iterations 5.4334071E-03 0.1141939 at 140iterations 3.0705209E-03 6.1311722E-02 at 150iterations 1.7287540E-03 3.3988953E-02 at 160iterations 9.7642338E-04 2.1039009E-02 at 170iterations 5.5620488E-04 1.1323214E-02 at 180iterations finished qdiffx linear iterations at : 18:49:18 total time elapsed so far: 12.20000 # loops : 180 mean,max change (kT/e) : 5.5620488E-04 1.1323214E-02 energy calculations done at 12.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.33000 DelPhi exited at 18:49:18 12.330u 0.210s 0:12.80 97.9% 0+0k 0+0io 0pf+0w