Sat Oct 8 16:11:35 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 16:11:35 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2397 !!! WARNING: ASL 35 has a net charge of -0.1000 !!! WARNING: GLM 41 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: 0.6555083 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): -1.853000 46.33600 ymin,ymax (A): -17.52300 29.58000 zmin,zma (A): -17.98300 36.32600 x,y,z range (A): 48.18900 47.10300 54.30900 scale (grids/A): 0.6555083 object centre (A): 22.24150 6.028500 9.171500 number of atom coordinates read : 2397 total number of charged atoms : 2333 net assigned charge : 3.806003 assigned positive charge : 360.8428 centred at (gu) : 90.80836 89.09425 90.37290 assigned negative charge : -357.0377 centred at (gu) : 90.86607 89.20447 90.42551 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7061 nv = 96 ne = 84 npr = 47688 no. pairs analyzed = 47688 no. exposed pairs = 2985 no. arc points = 20665 no. surface atoms = 1017 nbur = 1380 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 377 mr = 3986 m= 3 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 19 time to turn everything in is 0.2900000 number of dielectric boundary points 3403 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2014 ## 183 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8424 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5712336E-08 -1.1008269E-10 midg,1,midg; midg,igrid,midg 3.1644532E-08 -7.8037541E-09 1,midg,midg; igrid,midg,midg 1.5050897E-08 -1.1687565E-09 gauss-seidel spectral radius is 0.9879228 estimated iterations to convergence 74 setup time was (sec) 0.5100000 now iterating at: 16:11:36 rms-change max change #iterations 0.1567430 28.34109 at 10iterations 1.6424788E-02 2.446460 at 20iterations 1.7949863E-03 0.3050995 at 30iterations 2.1206801E-04 3.1790733E-02 at 40iterations 3.5428729E-05 5.9127808E-03 at 50iterations finished qdiffx linear iterations at : 16:11:38 total time elapsed so far: 2.970000 # loops : 50 mean,max change (kT/e) : 3.5428729E-05 5.9127808E-03 energy calculations done at 2.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.150000 DelPhi exited at 16:11:39 3.150u 0.138s 0:03.60 91.1% 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 16:11:39 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2397 !!! WARNING: ASL 35 has a net charge of -0.1000 !!! WARNING: GLM 41 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.966525 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): -1.853000 46.33600 ymin,ymax (A): -17.52300 29.58000 zmin,zma (A): -17.98300 36.32600 x,y,z range (A): 48.18900 47.10300 54.30900 scale (grids/A): 1.966525 object centre (A): 22.24150 6.028500 9.171500 number of atom coordinates read : 2397 total number of charged atoms : 2333 net assigned charge : 3.806003 assigned positive charge : 360.8428 centred at (gu) : 92.42458 87.28199 91.11799 assigned negative charge : -357.0377 centred at (gu) : 92.59785 87.61340 91.27656 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 76360 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20665 grid for indexing accessible points = 1.400000 m= 27985 mr = 53925 m= 4877 mr = 20828 m= 330 mr = 3309 m= 2 mr = 140 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 543 time to turn everything in is 0.5300000 number of dielectric boundary points 31352 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 114 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 18411 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) : 0.6555083 object centre at (A) : 22.24150 6.028500 9.171500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6744319E-02 -1.3577309E-02 midg,1,midg; midg,igrid,midg 2.8404655E-02 -4.2294227E-03 1,midg,midg; igrid,midg,midg 1.3784029E-02 -4.4303384E-02 gauss-seidel spectral radius is 0.9986992 estimated iterations to convergence 220 setup time was (sec) 0.7900000 now iterating at: 16:11:40 rms-change max change #iterations 4.344478 191.8082 at 10iterations 2.066744 83.12713 at 20iterations 0.9834771 31.04209 at 30iterations 0.4705841 14.47755 at 40iterations 0.2250932 6.980349 at 50iterations 0.1076199 3.313073 at 60iterations 5.1412594E-02 1.652407 at 70iterations 2.4514798E-02 0.7908993 at 80iterations 1.1725803E-02 0.3731308 at 90iterations 5.5902316E-03 0.1736193 at 100iterations 2.6898275E-03 8.8690281E-02 at 110iterations 1.2886566E-03 3.8778305E-02 at 120iterations finished qdiffx linear iterations at : 16:11:46 total time elapsed so far: 6.800000 # loops : 120 mean,max change (kT/e) : 1.2886566E-03 3.8778305E-02 energy calculations done at 6.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.970000 DelPhi exited at 16:11:46 6.972u 0.163s 0:07.43 95.9% 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 16:11:46 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2397 !!! WARNING: ASL 35 has a net charge of -0.1000 !!! WARNING: GLM 41 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.949787 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): -1.853000 46.33600 ymin,ymax (A): -17.52300 29.58000 zmin,zma (A): -17.98300 36.32600 x,y,z range (A): 48.18900 47.10300 54.30900 scale (grids/A): 2.949787 object centre (A): 22.24150 6.028500 9.171500 number of atom coordinates read : 2397 total number of charged atoms : 2333 net assigned charge : 3.806003 assigned positive charge : 360.8428 centred at (gu) : 93.63670 85.92290 91.67680 assigned negative charge : -357.0377 centred at (gu) : 93.89664 86.42009 91.91477 start vw surface at 0.1600000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 176548 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20665 grid for indexing accessible points = 1.400000 m= 89549 mr = 130209 m= 33920 mr = 73745 m= 9130 mr = 27833 m= 1454 mr = 7080 m= 112 mr = 1049 m= 4 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 1784 time to turn everything in is 1.360000 number of dielectric boundary points 70736 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 18663 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) : 1.966525 object centre at (A) : 22.24150 6.028500 9.171500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1712539 -0.2562203 midg,1,midg; midg,igrid,midg 0.2179702 -7.4722670E-02 1,midg,midg; igrid,midg,midg 0.1242140 -0.6302887 gauss-seidel spectral radius is 0.9992764 estimated iterations to convergence 293 setup time was (sec) 1.640000 now iterating at: 16:11:48 rms-change max change #iterations 10.00296 420.0583 at 10iterations 5.877554 134.7541 at 20iterations 3.444863 65.38866 at 30iterations 2.020081 39.72394 at 40iterations 1.176508 24.23971 at 50iterations 0.6873806 14.70298 at 60iterations 0.4002523 8.501482 at 70iterations 0.2325855 4.118158 at 80iterations 0.1351201 2.423170 at 90iterations 7.8267261E-02 1.479263 at 100iterations 4.5450456E-02 0.7730393 at 110iterations 2.6374722E-02 0.4652691 at 120iterations 1.5284349E-02 0.3341999 at 130iterations 8.8611990E-03 0.1618781 at 140iterations 5.1329713E-03 9.5549822E-02 at 150iterations 2.9839247E-03 5.2647114E-02 at 160iterations 1.7378744E-03 3.2873154E-02 at 170iterations 1.0183634E-03 1.9871712E-02 at 180iterations finished qdiffx linear iterations at : 16:11:58 total time elapsed so far: 11.24000 # loops : 180 mean,max change (kT/e) : 1.0183634E-03 1.9871712E-02 energy calculations done at 11.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.40000 DelPhi exited at 16:11:58 11.407u 0.172s 0:11.93 96.9% 0+0k 0+0io 0pf+0w