Sun Oct 9 07:44:36 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 Sun Oct 9 2011 at 07:44:36 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1699 !!! WARNING: NAP 202 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6940113 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): 5.338000 48.64100 ymin,ymax (A): -21.23900 21.53200 zmin,zma (A): -41.99300 9.302999 x,y,z range (A): 43.30300 42.77100 51.29600 scale (grids/A): 0.6940113 object centre (A): 26.98950 0.1464996 -16.34500 number of atom coordinates read : 1699 total number of charged atoms : 1562 net assigned charge : -10.49999 assigned positive charge : 251.7412 centred at (gu) : 89.63621 91.11985 90.06812 assigned negative charge : -262.2411 centred at (gu) : 89.75956 90.82121 89.83242 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5488 nv = 96 ne = 84 npr = 36701 no. pairs analyzed = 36701 no. exposed pairs = 2083 no. arc points = 14542 no. surface atoms = 712 nbur = 987 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 256 mr = 3062 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 97 time to turn everything in is 0.2100000 number of dielectric boundary points 2642 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1277 ## 108 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 6152 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3718373E-07 5.4660902E-09 midg,1,midg; midg,igrid,midg -1.2779911E-07 3.0704236E-08 1,midg,midg; igrid,midg,midg -2.9669023E-08 -9.6273318E-08 gauss-seidel spectral radius is 0.9891466 estimated iterations to convergence 78 setup time was (sec) 0.4300000 now iterating at: 07:44:37 rms-change max change #iterations 0.1727538 32.18008 at 10iterations 2.0172726E-02 3.192417 at 20iterations 2.3984921E-03 0.3534584 at 30iterations 2.7609561E-04 4.8023224E-02 at 40iterations 3.2742209E-05 5.4388046E-03 at 50iterations finished qdiffx linear iterations at : 07:44:39 total time elapsed so far: 2.840000 # loops : 50 mean,max change (kT/e) : 3.2742209E-05 5.4388046E-03 energy calculations done at 2.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.010000 DelPhi exited at 07:44:40 3.015u 0.148s 0:03.43 91.8% 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 Sun Oct 9 2011 at 07:44:40 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1699 !!! WARNING: NAP 202 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.082034 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): 5.338000 48.64100 ymin,ymax (A): -21.23900 21.53200 zmin,zma (A): -41.99300 9.302999 x,y,z range (A): 43.30300 42.77100 51.29600 scale (grids/A): 2.082034 object centre (A): 26.98950 0.1464996 -16.34500 number of atom coordinates read : 1699 total number of charged atoms : 1562 net assigned charge : -10.49999 assigned positive charge : 251.7412 centred at (gu) : 88.90864 93.35977 90.20441 assigned negative charge : -262.2411 centred at (gu) : 89.27869 92.46369 89.49715 start vw surface at 0.1300000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 58684 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14542 grid for indexing accessible points = 1.400000 m= 21328 mr = 40853 m= 3349 mr = 16169 m= 223 mr = 2218 m= 3 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 2957 time to turn everything in is 0.4300000 number of dielectric boundary points 24255 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 50 iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 12401 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) : 0.6940113 object centre at (A) : 26.98950 0.1464996 -16.34500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.2398196E-02 -1.0473828E-02 midg,1,midg; midg,igrid,midg -4.6019938E-02 3.6389489E-02 1,midg,midg; igrid,midg,midg -2.5337094E-02 -6.7958169E-02 gauss-seidel spectral radius is 0.9987513 estimated iterations to convergence 224 setup time was (sec) 0.6800000 now iterating at: 07:44:40 rms-change max change #iterations 4.046502 173.7085 at 10iterations 1.957869 71.76599 at 20iterations 0.9459661 33.28873 at 30iterations 0.4587928 15.54902 at 40iterations 0.2227691 7.623688 at 50iterations 0.1079416 3.715561 at 60iterations 5.2090287E-02 1.748164 at 70iterations 2.5206441E-02 0.9114056 at 80iterations 1.2176988E-02 0.4762337 at 90iterations 5.8810865E-03 0.2302946 at 100iterations 2.8610297E-03 9.5537186E-02 at 110iterations 1.3783509E-03 5.3573608E-02 at 120iterations finished qdiffx linear iterations at : 07:44:46 total time elapsed so far: 6.550000 # loops : 120 mean,max change (kT/e) : 1.3783509E-03 5.3573608E-02 energy calculations done at 6.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.720000 DelPhi exited at 07:44:47 6.723u 0.171s 0:07.15 96.3% 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 Sun Oct 9 2011 at 07:44:47 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1699 !!! WARNING: NAP 202 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.123051 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): 5.338000 48.64100 ymin,ymax (A): -21.23900 21.53200 zmin,zma (A): -41.99300 9.302999 x,y,z range (A): 43.30300 42.77100 51.29600 scale (grids/A): 3.123051 object centre (A): 26.98950 0.1464996 -16.34500 number of atom coordinates read : 1699 total number of charged atoms : 1562 net assigned charge : -10.49999 assigned positive charge : 251.7412 centred at (gu) : 88.36295 95.03964 90.30663 assigned negative charge : -262.2411 centred at (gu) : 88.91805 93.69569 89.24579 start vw surface at 0.1300000 fill in re-entrant regions at 0.6300000 boundary points on vw surface= 135566 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14542 grid for indexing accessible points = 1.400000 m= 68912 mr = 98661 m= 25188 mr = 57300 m= 6221 mr = 20857 m= 1082 mr = 4769 m= 67 mr = 798 m= 0 mr = 20 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 9428 time to turn everything in is 1.310000 number of dielectric boundary points 54631 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.430000 number of grid points assigned charge 12496 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) : 2.082034 object centre at (A) : 26.98950 0.1464996 -16.34500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.8227456 9.4728805E-02 midg,1,midg; midg,igrid,midg -0.3533389 0.4024960 1,midg,midg; igrid,midg,midg -0.1659348 -0.7544745 gauss-seidel spectral radius is 0.9992681 estimated iterations to convergence 292 setup time was (sec) 1.570000 now iterating at: 07:44:49 rms-change max change #iterations 9.138477 402.2942 at 10iterations 5.238801 119.1870 at 20iterations 3.009029 62.09803 at 30iterations 1.728697 31.92248 at 40iterations 0.9926276 19.97414 at 50iterations 0.5715767 11.28439 at 60iterations 0.3284007 6.592297 at 70iterations 0.1886633 3.750278 at 80iterations 0.1085404 2.091044 at 90iterations 6.2452357E-02 1.253283 at 100iterations 3.5784613E-02 0.7265415 at 110iterations 2.0606723E-02 0.4135551 at 120iterations 1.1859342E-02 0.2281278 at 130iterations 6.8296548E-03 0.1300812 at 140iterations 3.9248164E-03 7.9845190E-02 at 150iterations 2.2593921E-03 4.2216301E-02 at 160iterations 1.2980909E-03 2.4211884E-02 at 170iterations 7.4739801E-04 1.4707923E-02 at 180iterations finished qdiffx linear iterations at : 07:44:58 total time elapsed so far: 10.69000 # loops : 180 mean,max change (kT/e) : 7.4739801E-04 1.4707923E-02 energy calculations done at 10.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.87000 DelPhi exited at 07:44:58 10.869u 0.168s 0:11.35 97.0% 0+0k 0+0io 0pf+0w