Sat Oct 8 23:55:50 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 23:55:50 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2444 !!! WARNING: GLM 131 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6399194 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): -12.74300 40.71000 ymin,ymax (A): -30.41900 25.21300 zmin,zma (A): -9.639000 33.90500 x,y,z range (A): 53.45300 55.63200 43.54400 scale (grids/A): 0.6399194 object centre (A): 13.98350 -2.603000 12.13300 number of atom coordinates read : 2444 total number of charged atoms : 2305 net assigned charge : 11.40602 assigned positive charge : 356.1972 centred at (gu) : 89.68512 91.04856 90.32125 assigned negative charge : -344.7919 centred at (gu) : 89.65343 91.05978 90.25534 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6799 nv = 96 ne = 84 npr = 49248 no. pairs analyzed = 49248 no. exposed pairs = 3175 no. arc points = 23283 no. surface atoms = 1058 nbur = 1386 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 435 mr = 3585 m= 1 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 31 time to turn everything in is 0.2000000 number of dielectric boundary points 3608 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2222 ## 192 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8128 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.0975600E-09 2.4943915E-08 midg,1,midg; midg,igrid,midg 1.4270448E-08 1.9121277E-08 1,midg,midg; igrid,midg,midg 1.4147420E-08 1.8559508E-08 gauss-seidel spectral radius is 0.9873422 estimated iterations to convergence 73 setup time was (sec) 0.3900000 now iterating at: 23:55:51 rms-change max change #iterations 0.1411684 20.68274 at 10iterations 1.4011999E-02 2.014923 at 20iterations 1.4947809E-03 0.2114983 at 30iterations 2.4846889E-04 4.2633057E-02 at 40iterations 7.1070135E-05 1.3905525E-02 at 50iterations finished qdiffx linear iterations at : 23:55:54 total time elapsed so far: 3.510000 # loops : 50 mean,max change (kT/e) : 7.1070135E-05 1.3905525E-02 energy calculations done at 3.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.630000 DelPhi exited at 23:55:55 3.638u 0.225s 0:04.27 90.1% 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 23:55:55 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2444 !!! WARNING: GLM 131 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.919758 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): -12.74300 40.71000 ymin,ymax (A): -30.41900 25.21300 zmin,zma (A): -9.639000 33.90500 x,y,z range (A): 53.45300 55.63200 43.54400 scale (grids/A): 1.919758 object centre (A): 13.98350 -2.603000 12.13300 number of atom coordinates read : 2444 total number of charged atoms : 2305 net assigned charge : 11.40602 assigned positive charge : 356.1972 centred at (gu) : 89.05484 93.14529 90.96331 assigned negative charge : -344.7919 centred at (gu) : 88.96046 93.17942 90.76606 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 73225 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23283 grid for indexing accessible points = 1.400000 m= 25812 mr = 49367 m= 4197 mr = 18406 m= 265 mr = 2517 m= 2 mr = 91 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 2617 time to turn everything in is 0.3600000 number of dielectric boundary points 33120 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 171 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 18141 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) : 0.6399194 object centre at (A) : 13.98350 -2.603000 12.13300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1401506E-03 2.3129474E-02 midg,1,midg; midg,igrid,midg 4.0206254E-02 3.3937249E-02 1,midg,midg; igrid,midg,midg 5.0012793E-02 4.8587814E-02 gauss-seidel spectral radius is 0.9986510 estimated iterations to convergence 216 setup time was (sec) 0.5900000 now iterating at: 23:55:56 rms-change max change #iterations 4.065329 173.3839 at 10iterations 1.905482 66.48421 at 20iterations 0.8968804 30.45987 at 30iterations 0.4206553 13.76738 at 40iterations 0.1976915 6.143679 at 50iterations 9.2911087E-02 2.860721 at 60iterations 4.3645851E-02 1.290571 at 70iterations 2.0591546E-02 0.6592407 at 80iterations 9.7028166E-03 0.3042297 at 90iterations 4.6048262E-03 0.1694512 at 100iterations 2.2037730E-03 7.1809769E-02 at 110iterations 1.0767258E-03 3.8204193E-02 at 120iterations finished qdiffx linear iterations at : 23:56:03 total time elapsed so far: 8.420000 # loops : 120 mean,max change (kT/e) : 1.0767258E-03 3.8204193E-02 energy calculations done at 8.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.550000 DelPhi exited at 23:56:04 8.549u 0.231s 0:09.28 94.5% 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 23:56:04 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2444 !!! WARNING: GLM 131 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.879637 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): -12.74300 40.71000 ymin,ymax (A): -30.41900 25.21300 zmin,zma (A): -9.639000 33.90500 x,y,z range (A): 53.45300 55.63200 43.54400 scale (grids/A): 2.879637 object centre (A): 13.98350 -2.603000 12.13300 number of atom coordinates read : 2444 total number of charged atoms : 2305 net assigned charge : 11.40602 assigned positive charge : 356.1972 centred at (gu) : 88.58213 94.71787 91.44497 assigned negative charge : -344.7919 centred at (gu) : 88.44062 94.76908 91.14913 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 169277 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23283 grid for indexing accessible points = 1.400000 m= 83202 mr = 120083 m= 30422 mr = 66725 m= 7489 mr = 23849 m= 1122 mr = 5449 m= 76 mr = 717 m= 1 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 9039 time to turn everything in is 0.9400000 number of dielectric boundary points 74723 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 18439 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) : 1.919758 object centre at (A) : 13.98350 -2.603000 12.13300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.6077098E-03 0.2197088 midg,1,midg; midg,igrid,midg 0.5893261 0.3904287 1,midg,midg; igrid,midg,midg 0.4959548 0.5241580 gauss-seidel spectral radius is 0.9992700 estimated iterations to convergence 292 setup time was (sec) 1.170000 now iterating at: 23:56:05 rms-change max change #iterations 9.616916 399.4573 at 10iterations 5.676378 127.3049 at 20iterations 3.322974 81.78624 at 30iterations 1.935901 40.81962 at 40iterations 1.130690 23.55020 at 50iterations 0.6587284 15.69300 at 60iterations 0.3822355 7.370039 at 70iterations 0.2215111 4.239022 at 80iterations 0.1281886 2.421801 at 90iterations 7.4380733E-02 1.472229 at 100iterations 4.3065988E-02 0.8476582 at 110iterations 2.4915468E-02 0.4662342 at 120iterations 1.4420804E-02 0.2795563 at 130iterations 8.3557302E-03 0.1637206 at 140iterations 4.8311674E-03 9.8147869E-02 at 150iterations 2.8091213E-03 6.1197519E-02 at 160iterations 1.6436361E-03 3.0803680E-02 at 170iterations 9.7096205E-04 1.9821882E-02 at 180iterations finished qdiffx linear iterations at : 23:56:17 total time elapsed so far: 12.52000 # loops : 180 mean,max change (kT/e) : 9.7096205E-04 1.9821882E-02 energy calculations done at 12.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.66000 DelPhi exited at 23:56:17 12.659u 0.255s 0:13.44 95.9% 0+0k 0+0io 0pf+0w