Alternatively, making the initial path with PATHSAMPLE itself

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To run PATHSAMPLE with AMBER9, you need to have the following files in a directory together:

  • coords.prmtop - from setup (symmetrised)
  • coords.inpcrd - from setup (can be any structure, it is not used!)
  • min.in - as usual for the other OPTIM/GMIN runs
  • perm.allow - from setup
  • odata.start:
UPDATES 10000
BFGSCONV 1.0D-6
BFGSMIN 1.0D-6
CONVERGE 1.0D-6
BFGSSTEPS 60000
DEBUG
DUMPDATA
ENDHESS
MAXERISE 1.0D-4 1.0D0
DUMPALLPATHS
STEPS 400
NAB min1
  • min1 - the coords.1 file (if you used GMIN to generate endpoints) or a set of bare XYZ coordinates hacked from somewhere else... (maybe an OPTIM points.final file).
     3.55466675623289         3.16995629699793         1.54270798594802
     3.74753723250149         2.38942840233047         2.15184547061042
     4.17047717876711         3.93030795815968         1.78617683056756
     2.60386805295699         3.46607619676665         1.69960134494847
     3.73685649622452         2.77553090114839        0.123895029803436
     3.05032512058915         1.95214203202409       -0.786736327696273E-01
     3.35753139113690         3.91791869742228       -0.840504280699272
     2.30617919243626         4.17838802995329       -0.707688694615758
     3.96596515078617         4.80439047228292       -0.653169465698656
     3.50530517168077         3.59312703684487        -1.87189577557318
     5.14998969752088         2.21803054972706       -0.118519057183609
     5.32848416664402        0.995978917943404       -0.100324651337933
     6.15633697502413         3.08299331420796       -0.333025793368451
     5.93881982817854         4.06968704515201       -0.359551838035292
     7.57887293760818         2.71575857855800       -0.469528491560451
     7.67569566749208         2.02302478673195        -1.30623525156648
     8.38649561194879         3.98040568453036       -0.807315727170310
     7.94420445205871         4.45665448807773        -1.68406513918905
     8.30633077214107         4.68583450802602        0.214476997361609E-01
     9.85473280227943         3.72765387154945        -1.10114580198275
     10.2469598219409         3.24521826282487        -2.36509558341843
     9.50018457761475         3.05071206353910        -3.12384108206122
     11.6071325158249         3.01534996277546        -2.64455423147238
     11.9051878291689         2.64420970286146        -3.61747682547994
     12.5801817066824         3.26743026352440        -1.66087949639059
     13.6269130317628         3.09047449172246        -1.87578123663855
     12.1924529889115         3.74904973902444       -0.397640907207177
     12.9414713078565         3.94253331400061        0.360436563497512
     10.8322540264783         3.97886891829675       -0.118091695569543
     10.5377206130995         4.34750878884673        0.855785184894536
     8.13312305141417         1.99487549970490        0.778494881750552
     7.91746950457804         2.48841016169658         1.91162811585053
     8.77327437045932        0.929071062747699        0.621985551381477
  • min1.1 - a copy of min1
  • odata.finish:
UPDATES 10000
BFGSCONV 1.0D-6
BFGSMIN 1.0D-6
CONVERGE 1.0D-6
BFGSSTEPS 60000
DEBUG
DUMPDATA
ENDHESS
MAXERISE 1.0D-4 1.0D0
DUMPALLPATHS
STEPS 400
NAB min2
  • min2 - e.g. the coords.6 file (if you used GMIN to generate endpoints - the 6th lowest-energy minimum found).
     4.52890066837013         2.93656370927174       -0.239427010318513
     4.47801298280951         3.34682413410743        0.685745816669394
     3.82084445355726         3.35361741909884       -0.824222064556840
     4.34837994358002         1.94777782447867       -0.162163900364315
     5.87791690256576         3.17175818823496       -0.807102324278823
     6.61906995298852         2.74742829818315       -0.130655081327170
     6.02667092033151         2.45710681215281        -2.16358218545365
     5.95262363640866         1.37747131934317        -2.02436980239332
     5.24756512166076         2.78295535200078        -2.85510632117005
     6.99729664877394         2.68727253867928        -2.60030468636648
     6.16089968393573         4.68151689455798       -0.920411784320231
     5.62244016596902         5.33592039561112        -1.81712373251611
     6.98423529206534         5.31436725284026       -0.673951990813926E-01
     7.10773741232647         6.29500889192789       -0.278957541917429
     7.65002263961331         4.85384023396345         1.17638331169253
     7.79304148233171         5.75181584176790         1.77908060912197
     9.08133522523854         4.36004503952062        0.860210609132896
     9.64808200865552         5.21331212973193        0.483997210812589
     9.57024882175191         4.06764250691254         1.79035834788667
     9.22937876141801         3.22372157596704       -0.139790854541829
     9.07609759097414         1.88386125376228        0.267694210369426
     8.83769775081913         1.65471263441663         1.29726128270621
     9.24204378072364        0.836970355045778       -0.657982436133811
     9.12045749706307       -0.191318399305462       -0.340193609894010
     9.57860738401240         1.12343383132558        -1.99271869596955
     9.71214456395227        0.317301175588072        -2.70359380390128
     9.74823026781476         2.45802961662207        -2.40131565814173
     10.0126281167619         2.67971609186715        -3.42799452833696
     9.57042577860467         3.50529415247320        -1.47803452147272
     9.70343794144908         4.53061181135307        -1.79804418287749
     6.81377453554170         3.94839535602061         2.11621792418537
     5.56765424320609         4.07585398469793         2.10559458061561
     7.38509782472559         3.14717177778152         2.88894602214104

DIJINITSTART exp
COMMENT WARNING: DIJINITSTART runs overwrite all output, if in doubt, use DIJINITCONT 
COMMENT DIJINITCONT exp
TRIPLES
NATOMS         33
ETOL           1.0D-4
ITOL 1.0D1
GEOMDIFFTOL 1.0D-1
PLANCK 9.546E-14
TEMPERATURE   0.592
COMMENT MAXTSENERGY -80.0
COMMENT JOBSPERNODE    1
PBS
CONNECTIONS    1
COPYFILES perm.allow min.in coords.prmtop coords.inpcrd
COPYOPTIM
EXEC /home/csw34/bin/A9OPTIM
CYCLES 1000
PERMDIST
AMBER9

The DIJINITSTART keyword is the one that sets off OPTIM local minimizations for min1.1 and min2.2, takes those minima as the two end points, then tries iteratively to make a connected path between them by setting up and running some OPTIM connection-making jobs between likely pairs of minima. It analyses the output from those jobs and adds all the min-TS-min triples found to the growing database. The run will stop when you have made a fully connected discrete path between the end points.

The COPYOPTIM keyword is useful for debugging to see how well the connection-making attempts are doing. Have a look at the OPTIM.connect.* files, as described in Finding an initial path with OPTIM and starting up PATHSAMPLE. It is not a keyword that you want to leave in pathdata when doing the later sampling part of the calculations though as you'll get loads of random files cluttering up your working directory!!!

Also, make sure you set the full path of your A9OPTIM executable correctly on the EXEC line.

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