Mon Oct 10 13:55:21 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 13:55:21 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2317 !!! WARNING: HIT 84 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: 0.6484163 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): -30.45200 24.45100 ymin,ymax (A): 27.55800 70.29300 zmin,zma (A): -13.39900 41.11400 x,y,z range (A): 54.90300 42.73500 54.51300 scale (grids/A): 0.6484163 object centre (A): -3.000500 48.92550 13.85750 number of atom coordinates read : 2317 total number of charged atoms : 2183 net assigned charge : 10.51402 assigned positive charge : 338.4845 centred at (gu) : 91.26430 91.38342 89.40939 assigned negative charge : -327.9712 centred at (gu) : 91.29652 91.27264 89.42596 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6840 nv = 96 ne = 84 npr = 45682 no. pairs analyzed = 45682 no. exposed pairs = 3104 no. arc points = 22211 no. surface atoms = 1048 nbur = 1269 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 445 mr = 3625 m= 7 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3610 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2170 ## 184 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7931 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3976456E-08 1.5223813E-08 midg,1,midg; midg,igrid,midg 4.2436388E-09 4.3722306E-08 1,midg,midg; igrid,midg,midg 1.7880399E-08 1.9642300E-08 gauss-seidel spectral radius is 0.9876620 estimated iterations to convergence 74 setup time was (sec) 0.3700000 now iterating at: 13:55:22 rms-change max change #iterations 0.1418222 20.55188 at 10iterations 1.4600349E-02 2.247467 at 20iterations 1.6275232E-03 0.2136536 at 30iterations 2.6049602E-04 4.3182373E-02 at 40iterations 6.1549188E-05 1.1440277E-02 at 50iterations finished qdiffx linear iterations at : 13:55:25 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 6.1549188E-05 1.1440277E-02 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 13:55:25 3.378u 0.180s 0:03.89 91.2% 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 13:55:25 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2317 !!! WARNING: HIT 84 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: 1.945249 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): -30.45200 24.45100 ymin,ymax (A): 27.55800 70.29300 zmin,zma (A): -13.39900 41.11400 x,y,z range (A): 54.90300 42.73500 54.51300 scale (grids/A): 1.945249 object centre (A): -3.000500 48.92550 13.85750 number of atom coordinates read : 2317 total number of charged atoms : 2183 net assigned charge : 10.51402 assigned positive charge : 338.4845 centred at (gu) : 93.79267 94.14997 88.22793 assigned negative charge : -327.9712 centred at (gu) : 93.88959 93.81815 88.27793 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 72379 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22211 grid for indexing accessible points = 1.400000 m= 27461 mr = 48439 m= 5034 mr = 20087 m= 413 mr = 3241 m= 10 mr = 202 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 737 time to turn everything in is 0.3700000 number of dielectric boundary points 33328 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 148 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 17216 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) : 0.6484163 object centre at (A) : -3.000500 48.92550 13.85750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.3089147E-02 3.6876254E-02 midg,1,midg; midg,igrid,midg -2.0062036E-03 3.4648992E-02 1,midg,midg; igrid,midg,midg 5.5455945E-02 1.9192958E-02 gauss-seidel spectral radius is 0.9986731 estimated iterations to convergence 218 setup time was (sec) 0.5800000 now iterating at: 13:55:26 rms-change max change #iterations 4.031729 174.1444 at 10iterations 1.910506 64.31032 at 20iterations 0.9008754 36.43214 at 30iterations 0.4250804 13.55556 at 40iterations 0.2008157 7.175369 at 50iterations 9.4867274E-02 3.236089 at 60iterations 4.4883426E-02 1.416871 at 70iterations 2.1298643E-02 0.6758775 at 80iterations 1.0091404E-02 0.3215877 at 90iterations 4.8121363E-03 0.1499777 at 100iterations 2.2975469E-03 7.3499680E-02 at 110iterations 1.1124562E-03 3.8232803E-02 at 120iterations finished qdiffx linear iterations at : 13:55:33 total time elapsed so far: 7.690000 # loops : 120 mean,max change (kT/e) : 1.1124562E-03 3.8232803E-02 energy calculations done at 7.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.820000 DelPhi exited at 13:55:33 7.822u 0.195s 0:08.29 96.6% 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 13:55:34 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2317 !!! WARNING: HIT 84 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: 2.917873 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): -30.45200 24.45100 ymin,ymax (A): 27.55800 70.29300 zmin,zma (A): -13.39900 41.11400 x,y,z range (A): 54.90300 42.73500 54.51300 scale (grids/A): 2.917873 object centre (A): -3.000500 48.92550 13.85750 number of atom coordinates read : 2317 total number of charged atoms : 2183 net assigned charge : 10.51402 assigned positive charge : 338.4845 centred at (gu) : 95.68892 96.22485 87.34180 assigned negative charge : -327.9712 centred at (gu) : 95.83436 95.72717 87.41695 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 166947 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22211 grid for indexing accessible points = 1.400000 m= 85293 mr = 117344 m= 33713 mr = 69123 m= 9224 mr = 27076 m= 1652 mr = 6992 m= 183 mr = 1202 m= 6 mr = 105 m= 0 mr = 0 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 2570 time to turn everything in is 0.9600000 number of dielectric boundary points 75176 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.060000 number of grid points assigned charge 17464 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) : 1.945249 object centre at (A) : -3.000500 48.92550 13.85750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6360763 0.3652724 midg,1,midg; midg,igrid,midg -1.2264044E-02 0.3372333 1,midg,midg; igrid,midg,midg 0.7296399 0.2374849 gauss-seidel spectral radius is 0.9992765 estimated iterations to convergence 293 setup time was (sec) 1.210000 now iterating at: 13:55:35 rms-change max change #iterations 9.685270 330.3843 at 10iterations 5.739831 146.3635 at 20iterations 3.383512 71.67804 at 30iterations 1.982787 45.67961 at 40iterations 1.157531 27.75056 at 50iterations 0.6759160 13.81369 at 60iterations 0.3945837 7.976445 at 70iterations 0.2296406 4.764524 at 80iterations 0.1331369 2.328697 at 90iterations 7.7243209E-02 1.492647 at 100iterations 4.4758670E-02 0.8737030 at 110iterations 2.6067888E-02 0.4756927 at 120iterations 1.5074935E-02 0.2885151 at 130iterations 8.7382514E-03 0.1694546 at 140iterations 5.0559468E-03 9.5310211E-02 at 150iterations 2.9311888E-03 6.2690258E-02 at 160iterations 1.6997263E-03 3.1623840E-02 at 170iterations 9.8765432E-04 1.8417358E-02 at 180iterations finished qdiffx linear iterations at : 13:55:46 total time elapsed so far: 12.53000 # loops : 180 mean,max change (kT/e) : 9.8765432E-04 1.8417358E-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 13:55:47 12.662u 0.193s 0:13.13 97.8% 0+0k 0+0io 0pf+0w