Sat Oct 8 14:09:05 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 Sat Oct 8 2011 at 14:09:05 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2943 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 316 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6319340 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): -11.39600 43.31500 ymin,ymax (A): 10.28200 55.09800 zmin,zma (A): 36.32000 92.65500 x,y,z range (A): 54.71100 44.81600 56.33500 scale (grids/A): 0.6319340 object centre (A): 15.95950 32.69000 64.48750 number of atom coordinates read : 2943 total number of charged atoms : 2797 net assigned charge : -1.985991 assigned positive charge : 440.9857 centred at (gu) : 89.18439 89.64948 91.94683 assigned negative charge : -442.9724 centred at (gu) : 89.16911 89.56303 91.90732 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7930 nv = 96 ne = 84 npr = 61300 no. pairs analyzed = 61300 no. exposed pairs = 3403 no. arc points = 23208 no. surface atoms = 1160 nbur = 1783 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 408 mr = 4690 m= 4 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 3609 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2304 ## 198 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 9562 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.2981947E-09 2.9563461E-09 midg,1,midg; midg,igrid,midg -1.2492285E-08 6.2589303E-09 1,midg,midg; igrid,midg,midg -4.6900630E-09 -5.9824018E-10 gauss-seidel spectral radius is 0.9870535 estimated iterations to convergence 72 setup time was (sec) 0.6600000 now iterating at: 14:09:06 rms-change max change #iterations 0.1531910 27.23598 at 10iterations 1.5143220E-02 1.859703 at 20iterations 1.5845611E-03 0.2048645 at 30iterations 2.0121603E-04 2.7755737E-02 at 40iterations 3.5186251E-05 5.1832199E-03 at 50iterations finished qdiffx linear iterations at : 14:09:10 total time elapsed so far: 4.040000 # loops : 50 mean,max change (kT/e) : 3.5186251E-05 5.1832199E-03 energy calculations done at 4.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.220000 DelPhi exited at 14:09:10 4.228u 0.286s 0:04.77 94.3% 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 Sat Oct 8 2011 at 14:09:10 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2943 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 316 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.895802 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): -11.39600 43.31500 ymin,ymax (A): 10.28200 55.09800 zmin,zma (A): 36.32000 92.65500 x,y,z range (A): 54.71100 44.81600 56.33500 scale (grids/A): 1.895802 object centre (A): 15.95950 32.69000 64.48750 number of atom coordinates read : 2943 total number of charged atoms : 2797 net assigned charge : -1.985991 assigned positive charge : 440.9857 centred at (gu) : 87.55258 88.94760 95.84033 assigned negative charge : -442.9724 centred at (gu) : 87.50711 88.68844 95.72168 start vw surface at 0.1500000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 86609 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23208 grid for indexing accessible points = 1.400000 m= 32038 mr = 63039 m= 4776 mr = 24387 m= 230 mr = 2917 m= 1 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 124 time to turn everything in is 0.7400000 number of dielectric boundary points 33232 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 142 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 21973 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) : 0.6319340 object centre at (A) : 15.95950 32.69000 64.48750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4519722E-02 -2.4666737E-03 midg,1,midg; midg,igrid,midg -1.7950686E-03 1.2067583E-02 1,midg,midg; igrid,midg,midg -1.4134559E-02 6.5225130E-03 gauss-seidel spectral radius is 0.9986516 estimated iterations to convergence 216 setup time was (sec) 1.040000 now iterating at: 14:09:12 rms-change max change #iterations 4.585331 184.9196 at 10iterations 2.162248 68.00435 at 20iterations 1.020124 30.22591 at 30iterations 0.4784927 14.41581 at 40iterations 0.2264207 7.407661 at 50iterations 0.1066961 3.287746 at 60iterations 5.0230090E-02 1.517251 at 70iterations 2.3671852E-02 0.6877441 at 80iterations 1.1220139E-02 0.3298016 at 90iterations 5.2994327E-03 0.1537857 at 100iterations 2.5083788E-03 7.6389313E-02 at 110iterations 1.1890106E-03 3.6956787E-02 at 120iterations finished qdiffx linear iterations at : 14:09:20 total time elapsed so far: 9.680000 # loops : 120 mean,max change (kT/e) : 1.1890106E-03 3.6956787E-02 energy calculations done at 9.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.860000 DelPhi exited at 14:09:21 9.863u 0.356s 0:10.47 97.5% 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 Sat Oct 8 2011 at 14:09:21 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2943 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 316 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.843703 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): -11.39600 43.31500 ymin,ymax (A): 10.28200 55.09800 zmin,zma (A): 36.32000 92.65500 x,y,z range (A): 54.71100 44.81600 56.33500 scale (grids/A): 2.843703 object centre (A): 15.95950 32.69000 64.48750 number of atom coordinates read : 2943 total number of charged atoms : 2797 net assigned charge : -1.985991 assigned positive charge : 440.9857 centred at (gu) : 86.32891 88.42133 98.76038 assigned negative charge : -442.9724 centred at (gu) : 86.26063 88.03257 98.58256 start vw surface at 0.1600000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 200387 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23208 grid for indexing accessible points = 1.400000 m= 104667 mr = 152051 m= 37501 mr = 87700 m= 8529 mr = 30665 m= 1110 mr = 6254 m= 37 mr = 690 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 1.200000 no. cavity mid-points inaccessible to solvent = 406 time to turn everything in is 1.960000 number of dielectric boundary points 74863 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.120000 number of grid points assigned charge 22376 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) : 1.895802 object centre at (A) : 15.95950 32.69000 64.48750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0526349E-02 4.6994571E-02 midg,1,midg; midg,igrid,midg -9.3867141E-04 0.1621148 1,midg,midg; igrid,midg,midg 3.7857581E-02 0.2674747 gauss-seidel spectral radius is 0.9992665 estimated iterations to convergence 291 setup time was (sec) 2.300000 now iterating at: 14:09:23 rms-change max change #iterations 10.68852 387.5385 at 10iterations 6.290134 143.6021 at 20iterations 3.669919 70.07503 at 30iterations 2.135569 39.94892 at 40iterations 1.239515 29.61020 at 50iterations 0.7177028 13.09827 at 60iterations 0.4162737 7.094849 at 70iterations 0.2406525 4.517057 at 80iterations 0.1390318 2.358101 at 90iterations 8.0410309E-02 1.385712 at 100iterations 4.6449050E-02 0.8356285 at 110iterations 2.6838582E-02 0.4774818 at 120iterations 1.5465539E-02 0.2755661 at 130iterations 8.9488178E-03 0.1572845 at 140iterations 5.1745810E-03 8.5048676E-02 at 150iterations 2.9933848E-03 5.0913334E-02 at 160iterations 1.7401800E-03 2.7706146E-02 at 170iterations 1.0171066E-03 1.7906189E-02 at 180iterations finished qdiffx linear iterations at : 14:09:38 total time elapsed so far: 16.76000 # loops : 180 mean,max change (kT/e) : 1.0171066E-03 1.7906189E-02 energy calculations done at 16.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.96000 DelPhi exited at 14:09:38 16.960u 0.349s 0:17.56 98.5% 0+0k 0+0io 0pf+0w