Tue Oct 11 01:46:26 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 01:46:26 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2667 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5916570 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): 17.92500 78.09500 ymin,ymax (A): -11.47600 44.47300 zmin,zma (A): -7.648000 35.28300 x,y,z range (A): 60.17000 55.94900 42.93100 scale (grids/A): 0.5916570 object centre (A): 48.01000 16.49850 13.81750 number of atom coordinates read : 2667 total number of charged atoms : 2516 net assigned charge : 6.312019 assigned positive charge : 402.3537 centred at (gu) : 88.25243 89.81773 89.75335 assigned negative charge : -396.0424 centred at (gu) : 88.52363 89.96437 89.90672 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6096 nv = 96 ne = 84 npr = 54228 no. pairs analyzed = 54228 no. exposed pairs = 3215 no. arc points = 22691 no. surface atoms = 1090 nbur = 1577 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 278 mr = 3364 m= 1 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.3500000 number of dielectric boundary points 2982 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2234 ## 245 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 7651 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.5627384E-09 -2.4229867E-09 midg,1,midg; midg,igrid,midg 6.2721446E-09 -2.2702404E-09 1,midg,midg; igrid,midg,midg 1.4155469E-08 -4.0465844E-09 gauss-seidel spectral radius is 0.9852206 estimated iterations to convergence 67 setup time was (sec) 0.6200000 now iterating at: 01:46:27 rms-change max change #iterations 0.1055093 15.87510 at 10iterations 9.3582971E-03 1.614044 at 20iterations 1.0424018E-03 0.2156868 at 30iterations 2.0083852E-04 4.6894073E-02 at 40iterations 4.2786254E-05 1.0696411E-02 at 50iterations finished qdiffx linear iterations at : 01:46:30 total time elapsed so far: 3.950000 # loops : 50 mean,max change (kT/e) : 4.2786254E-05 1.0696411E-02 energy calculations done at 3.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.130000 DelPhi exited at 01:46:31 4.135u 0.283s 0:05.02 87.8% 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 01:46:31 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2667 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.774971 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): 17.92500 78.09500 ymin,ymax (A): -11.47600 44.47300 zmin,zma (A): -7.648000 35.28300 x,y,z range (A): 60.17000 55.94900 42.93100 scale (grids/A): 1.774971 object centre (A): 48.01000 16.49850 13.81750 number of atom coordinates read : 2667 total number of charged atoms : 2516 net assigned charge : 6.312019 assigned positive charge : 402.3537 centred at (gu) : 84.75656 89.45261 89.25958 assigned negative charge : -396.0424 centred at (gu) : 85.57066 89.89301 89.71998 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 66449 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22691 grid for indexing accessible points = 1.400000 m= 21830 mr = 46128 m= 2869 mr = 15905 m= 126 mr = 1770 m= 0 mr = 29 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 3252 time to turn everything in is 0.6000000 number of dielectric boundary points 27442 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 201 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 19582 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) : 0.5916570 object centre at (A) : 48.01000 16.49850 13.81750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2404492E-02 1.0050386E-03 midg,1,midg; midg,igrid,midg 2.5443915E-02 -2.1654479E-02 1,midg,midg; igrid,midg,midg 5.7924534E-03 -4.6820478E-03 gauss-seidel spectral radius is 0.9984335 estimated iterations to convergence 200 setup time was (sec) 0.8900000 now iterating at: 01:46:32 rms-change max change #iterations 3.722768 155.5000 at 10iterations 1.654975 68.08614 at 20iterations 0.7328230 29.39741 at 30iterations 0.3235597 12.51188 at 40iterations 0.1437332 4.777260 at 50iterations 6.4010188E-02 2.225993 at 60iterations 2.8550168E-02 1.019348 at 70iterations 1.2755711E-02 0.4436188 at 80iterations 5.7727951E-03 0.2071095 at 90iterations 2.6635549E-03 9.9157333E-02 at 100iterations 1.2783105E-03 4.7538757E-02 at 110iterations 6.4342807E-04 2.9060364E-02 at 120iterations finished qdiffx linear iterations at : 01:46:40 total time elapsed so far: 9.200000 # loops : 120 mean,max change (kT/e) : 6.4342807E-04 2.9060364E-02 energy calculations done at 9.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.380000 DelPhi exited at 01:46:41 9.379u 0.312s 0:10.14 95.4% 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 Tue Oct 11 2011 at 01:46:41 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2667 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.662457 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): 17.92500 78.09500 ymin,ymax (A): -11.47600 44.47300 zmin,zma (A): -7.648000 35.28300 x,y,z range (A): 60.17000 55.94900 42.93100 scale (grids/A): 2.662457 object centre (A): 48.01000 16.49850 13.81750 number of atom coordinates read : 2667 total number of charged atoms : 2516 net assigned charge : 6.312019 assigned positive charge : 402.3537 centred at (gu) : 82.13472 89.17873 88.88917 assigned negative charge : -396.0424 centred at (gu) : 83.35603 89.83956 89.57987 start vw surface at 0.1600000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 154372 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22691 grid for indexing accessible points = 1.400000 m= 73338 mr = 112247 m= 23763 mr = 59675 m= 5084 mr = 19058 m= 549 mr = 3813 m= 17 mr = 370 m= 0 mr = 4 time to grow re-entrant surface = 0.8500001 no. cavity mid-points inaccessible to solvent = 10603 time to turn everything in is 1.470000 number of dielectric boundary points 61956 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.620000 number of grid points assigned charge 20124 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) : 1.774971 object centre at (A) : 48.01000 16.49850 13.81750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2420003 1.9427858E-02 midg,1,midg; midg,igrid,midg 0.3046561 -0.4482795 1,midg,midg; igrid,midg,midg 1.4054683E-02 0.1004112 gauss-seidel spectral radius is 0.9991999 estimated iterations to convergence 279 setup time was (sec) 1.790000 now iterating at: 01:46:43 rms-change max change #iterations 8.978837 282.8400 at 10iterations 5.107049 111.9572 at 20iterations 2.876534 63.00928 at 30iterations 1.617613 33.82631 at 40iterations 0.9113405 18.96840 at 50iterations 0.5117080 10.14269 at 60iterations 0.2879887 5.475315 at 70iterations 0.1613248 3.253120 at 80iterations 9.0861075E-02 2.004217 at 90iterations 5.1040541E-02 0.9792233 at 100iterations 2.8736385E-02 0.6845875 at 110iterations 1.6240850E-02 0.3612776 at 120iterations 9.2204018E-03 0.1954117 at 130iterations 5.2771247E-03 0.1130562 at 140iterations 3.0702048E-03 7.1113586E-02 at 150iterations 1.8380220E-03 4.7561646E-02 at 160iterations 1.1480803E-03 3.0841827E-02 at 170iterations 7.5081142E-04 2.0599365E-02 at 180iterations finished qdiffx linear iterations at : 01:46:57 total time elapsed so far: 15.30000 # loops : 180 mean,max change (kT/e) : 7.5081142E-04 2.0599365E-02 energy calculations done at 15.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.48000 DelPhi exited at 01:46:57 15.483u 0.340s 0:16.56 95.5% 0+0k 0+0io 0pf+0w