Mon Oct 10 14:03:42 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 14:03:42 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2147 !!! WARNING: LYS 224 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6714321 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): -19.18200 33.83900 ymin,ymax (A): -26.92000 20.17500 zmin,zma (A): -6.290000 41.96900 x,y,z range (A): 53.02100 47.09500 48.25900 scale (grids/A): 0.6714321 object centre (A): 7.328498 -3.372500 17.83950 number of atom coordinates read : 2147 total number of charged atoms : 2005 net assigned charge : -9.271976 assigned positive charge : 322.0198 centred at (gu) : 88.43222 91.65498 88.12045 assigned negative charge : -331.2920 centred at (gu) : 88.73991 91.71769 88.12845 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6574 nv = 96 ne = 84 npr = 44023 no. pairs analyzed = 44023 no. exposed pairs = 2714 no. arc points = 19415 no. surface atoms = 911 nbur = 1236 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 384 mr = 3579 m= 2 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 16 time to turn everything in is 0.3000000 number of dielectric boundary points 3323 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1808 ## 148 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7528 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.4685748E-08 -2.3737105E-08 midg,1,midg; midg,igrid,midg -1.3646594E-08 -6.5245082E-08 1,midg,midg; igrid,midg,midg 4.8143509E-08 -7.5181561E-08 gauss-seidel spectral radius is 0.9884616 estimated iterations to convergence 76 setup time was (sec) 0.5900000 now iterating at: 14:03:43 rms-change max change #iterations 0.1659954 23.82095 at 10iterations 1.7786639E-02 2.505661 at 20iterations 1.9677486E-03 0.2783318 at 30iterations 2.1958030E-04 3.1848907E-02 at 40iterations 2.4137467E-05 3.6010742E-03 at 50iterations finished qdiffx linear iterations at : 14:03:46 total time elapsed so far: 4.140000 # loops : 50 mean,max change (kT/e) : 2.4137467E-05 3.6010742E-03 energy calculations done at 4.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.320000 DelPhi exited at 14:03:47 4.327u 0.299s 0:05.14 89.6% 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 14:03:47 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2147 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 2.014296 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): -19.18200 33.83900 ymin,ymax (A): -26.92000 20.17500 zmin,zma (A): -6.290000 41.96900 x,y,z range (A): 53.02100 47.09500 48.25900 scale (grids/A): 2.014296 object centre (A): 7.328498 -3.372500 17.83950 number of atom coordinates read : 2147 total number of charged atoms : 2005 net assigned charge : -9.271976 assigned positive charge : 322.0198 centred at (gu) : 85.29644 94.96480 84.36140 assigned negative charge : -331.2920 centred at (gu) : 86.21962 95.15312 84.38528 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 69662 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19415 grid for indexing accessible points = 1.400000 m= 26288 mr = 47420 m= 4520 mr = 19694 m= 286 mr = 2882 m= 4 mr = 130 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 770 time to turn everything in is 0.5300000 number of dielectric boundary points 30634 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 98 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 15844 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) : 0.6714321 object centre at (A) : 7.328498 -3.372500 17.83950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2095287E-02 -2.6965123E-02 midg,1,midg; midg,igrid,midg -1.1219017E-02 -2.1530638E-02 1,midg,midg; igrid,midg,midg 5.1529426E-03 -9.2873015E-02 gauss-seidel spectral radius is 0.9987269 estimated iterations to convergence 222 setup time was (sec) 0.8500000 now iterating at: 14:03:48 rms-change max change #iterations 4.274468 208.5626 at 10iterations 2.053896 77.16153 at 20iterations 0.9836584 35.48450 at 30iterations 0.4710706 14.98365 at 40iterations 0.2265183 8.117111 at 50iterations 0.1085852 3.699409 at 60iterations 5.2219987E-02 1.760213 at 70iterations 2.5086069E-02 0.7575970 at 80iterations 1.2032432E-02 0.4327135 at 90iterations 5.7829539E-03 0.1924479 at 100iterations 2.7740814E-03 8.1935883E-02 at 110iterations 1.3329759E-03 4.8400879E-02 at 120iterations finished qdiffx linear iterations at : 14:03:56 total time elapsed so far: 9.130000 # loops : 120 mean,max change (kT/e) : 1.3329759E-03 4.8400879E-02 energy calculations done at 9.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.320000 DelPhi exited at 14:03:57 9.324u 0.259s 0:10.11 94.6% 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 14:03:57 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2147 !!! WARNING: LYS 224 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.021445 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): -19.18200 33.83900 ymin,ymax (A): -26.92000 20.17500 zmin,zma (A): -6.290000 41.96900 x,y,z range (A): 53.02100 47.09500 48.25900 scale (grids/A): 3.021445 object centre (A): 7.328498 -3.372500 17.83950 number of atom coordinates read : 2147 total number of charged atoms : 2005 net assigned charge : -9.271976 assigned positive charge : 322.0198 centred at (gu) : 82.94465 97.44724 81.54200 assigned negative charge : -331.2920 centred at (gu) : 84.32947 97.72968 81.57803 start vw surface at 0.1600000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 160881 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19415 grid for indexing accessible points = 1.400000 m= 82572 mr = 115022 m= 32325 mr = 67601 m= 8198 mr = 26517 m= 1195 mr = 6242 m= 79 mr = 810 m= 1 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 2699 time to turn everything in is 1.450000 number of dielectric boundary points 69019 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.600000 number of grid points assigned charge 16040 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) : 2.014296 object centre at (A) : 7.328498 -3.372500 17.83950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.8673446E-02 -0.3020383 midg,1,midg; midg,igrid,midg -7.3561423E-02 -0.1524530 1,midg,midg; igrid,midg,midg 0.1557640 -0.8829090 gauss-seidel spectral radius is 0.9992766 estimated iterations to convergence 293 setup time was (sec) 1.790000 now iterating at: 14:03:59 rms-change max change #iterations 9.842338 429.1843 at 10iterations 5.722091 125.1093 at 20iterations 3.311629 64.95825 at 30iterations 1.919376 38.76907 at 40iterations 1.110156 21.20151 at 50iterations 0.6430811 13.35259 at 60iterations 0.3711174 6.947021 at 70iterations 0.2149387 4.036302 at 80iterations 0.1238624 2.423230 at 90iterations 7.1653962E-02 1.461258 at 100iterations 4.1345105E-02 0.7646074 at 110iterations 2.3921795E-02 0.4438829 at 120iterations 1.3782478E-02 0.2475014 at 130iterations 7.9677664E-03 0.1476727 at 140iterations 4.5978045E-03 8.5430145E-02 at 150iterations 2.6501291E-03 5.0272703E-02 at 160iterations 1.5337202E-03 2.6023865E-02 at 170iterations 8.8725140E-04 1.6978264E-02 at 180iterations finished qdiffx linear iterations at : 14:04:12 total time elapsed so far: 14.85000 # loops : 180 mean,max change (kT/e) : 8.8725140E-04 1.6978264E-02 energy calculations done at 14.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.03000 DelPhi exited at 14:04:13 15.033u 0.279s 0:15.96 95.8% 0+0k 0+0io 0pf+0w