Tue Oct 11 01:10:45 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 01:10:45 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2740 !!! 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: 0.6321135 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): -4.947000 51.37200 ymin,ymax (A): -16.15700 29.77200 zmin,zma (A): 56.87200 109.7430 x,y,z range (A): 56.31900 45.92900 52.87101 scale (grids/A): 0.6321135 object centre (A): 23.21250 6.807501 83.30750 number of atom coordinates read : 2740 total number of charged atoms : 2588 net assigned charge : 4.312016 assigned positive charge : 413.2957 centred at (gu) : 89.82510 90.14355 89.07420 assigned negative charge : -408.9842 centred at (gu) : 90.08170 90.05837 89.10526 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7272 nv = 96 ne = 84 npr = 55631 no. pairs analyzed = 55631 no. exposed pairs = 3290 no. arc points = 23083 no. surface atoms = 1119 nbur = 1621 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 375 mr = 4091 m= 2 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.3600000 number of dielectric boundary points 3526 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2230 ## 210 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8740 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.7511297E-09 1.5564108E-09 midg,1,midg; midg,igrid,midg -3.4475836E-09 1.3695863E-08 1,midg,midg; igrid,midg,midg 3.0753686E-08 -2.0356611E-08 gauss-seidel spectral radius is 0.9870467 estimated iterations to convergence 72 setup time was (sec) 0.6200000 now iterating at: 01:10:46 rms-change max change #iterations 0.1414482 18.90344 at 10iterations 1.4931753E-02 2.180843 at 20iterations 1.8837504E-03 0.3187218 at 30iterations 4.1276630E-04 8.5834503E-02 at 40iterations 1.1146592E-04 2.4211884E-02 at 50iterations finished qdiffx linear iterations at : 01:10:49 total time elapsed so far: 3.880000 # loops : 50 mean,max change (kT/e) : 1.1146592E-04 2.4211884E-02 energy calculations done at 3.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.060000 DelPhi exited at 01:10:49 4.060u 0.265s 0:04.83 89.4% 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 01:10:50 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2740 !!! 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: 1.896340 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): -4.947000 51.37200 ymin,ymax (A): -16.15700 29.77200 zmin,zma (A): 56.87200 109.7430 x,y,z range (A): 56.31900 45.92900 52.87101 scale (grids/A): 1.896340 object centre (A): 23.21250 6.807501 83.30750 number of atom coordinates read : 2740 total number of charged atoms : 2588 net assigned charge : 4.312016 assigned positive charge : 413.2957 centred at (gu) : 89.47441 90.43009 87.22211 assigned negative charge : -408.9842 centred at (gu) : 90.24479 90.17469 87.31533 start vw surface at 0.1700000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 79128 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23083 grid for indexing accessible points = 1.400000 m= 28031 mr = 55505 m= 4177 mr = 20832 m= 213 mr = 2657 m= 3 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 467 time to turn everything in is 0.6900000 number of dielectric boundary points 32500 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 170 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 20328 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) : 0.6321135 object centre at (A) : 23.21250 6.807501 83.30750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.9158526E-03 1.5952207E-02 midg,1,midg; midg,igrid,midg 1.1389805E-02 1.9893207E-02 1,midg,midg; igrid,midg,midg 4.0814035E-02 -3.9132748E-02 gauss-seidel spectral radius is 0.9986347 estimated iterations to convergence 214 setup time was (sec) 0.9900000 now iterating at: 01:10:51 rms-change max change #iterations 4.389224 194.3484 at 10iterations 2.052952 68.94372 at 20iterations 0.9602889 32.76354 at 30iterations 0.4494594 16.14765 at 40iterations 0.2111512 6.055256 at 50iterations 9.8886840E-02 3.385160 at 60iterations 4.6541207E-02 1.465327 at 70iterations 2.1895662E-02 0.6611996 at 80iterations 1.0389904E-02 0.3128357 at 90iterations 4.9922364E-03 0.1687698 at 100iterations 2.4653242E-03 8.0291748E-02 at 110iterations 1.2717664E-03 4.8786163E-02 at 120iterations finished qdiffx linear iterations at : 01:10:59 total time elapsed so far: 9.220000 # loops : 120 mean,max change (kT/e) : 1.2717664E-03 4.8786163E-02 energy calculations done at 9.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.400000 DelPhi exited at 01:11:00 9.405u 0.272s 0:10.05 96.2% 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 01:11:00 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2740 !!! 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: 2.844511 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): -4.947000 51.37200 ymin,ymax (A): -16.15700 29.77200 zmin,zma (A): 56.87200 109.7430 x,y,z range (A): 56.31900 45.92900 52.87101 scale (grids/A): 2.844511 object centre (A): 23.21250 6.807501 83.30750 number of atom coordinates read : 2740 total number of charged atoms : 2588 net assigned charge : 4.312016 assigned positive charge : 413.2957 centred at (gu) : 89.21159 90.64480 85.83305 assigned negative charge : -408.9842 centred at (gu) : 90.36716 90.26192 85.97276 start vw surface at 0.1700000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 183049 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23083 grid for indexing accessible points = 1.400000 m= 91926 mr = 134457 m= 32203 mr = 75625 m= 7439 mr = 25952 m= 896 mr = 5592 m= 37 mr = 574 m= 0 mr = 6 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 1679 time to turn everything in is 1.790000 number of dielectric boundary points 73344 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.940000 number of grid points assigned charge 20703 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) : 1.896340 object centre at (A) : 23.21250 6.807501 83.30750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.4732646E-02 0.1723597 midg,1,midg; midg,igrid,midg 0.1807220 0.2198926 1,midg,midg; igrid,midg,midg 0.4898715 -0.2257401 gauss-seidel spectral radius is 0.9992558 estimated iterations to convergence 289 setup time was (sec) 2.110000 now iterating at: 01:11:02 rms-change max change #iterations 10.14813 409.3414 at 10iterations 5.888385 129.6181 at 20iterations 3.399972 83.76026 at 30iterations 1.960672 37.25651 at 40iterations 1.128467 23.37575 at 50iterations 0.6489887 12.02469 at 60iterations 0.3729874 6.420725 at 70iterations 0.2144264 3.862179 at 80iterations 0.1230612 2.059826 at 90iterations 7.0876800E-02 1.232248 at 100iterations 4.0624302E-02 0.6969910 at 110iterations 2.3379304E-02 0.4128799 at 120iterations 1.3502843E-02 0.2518845 at 130iterations 7.8493599E-03 0.1478081 at 140iterations 4.6123224E-03 8.8405609E-02 at 150iterations 2.7549427E-03 5.8341980E-02 at 160iterations 1.7037790E-03 3.7673950E-02 at 170iterations 1.1070808E-03 2.5016785E-02 at 180iterations finished qdiffx linear iterations at : 01:11:16 total time elapsed so far: 15.60000 # loops : 180 mean,max change (kT/e) : 1.1070808E-03 2.5016785E-02 energy calculations done at 15.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.78000 DelPhi exited at 01:11:16 15.786u 0.281s 0:16.51 97.2% 0+0k 0+0io 0pf+0w