Department of Chemistry and Chemical Biology

AMBER BUGS -- NOT FIXED

Some bugs are known and not fixed, and may never be fixed for a variety of reasons. If you fix one, please let us know at amber-request@cgl.ucsf.edu so we can test and install your fix as well as announce it (with full attribution!) on the amber reflector.
  • The "deviations from ideal bond lengths and angles" reported in NMR refinements in MPI versions of sander are not correct. Run a final step on a single-processor to get the correct values.

  • Resp does not work when compiled on R4400 machines under IRIX 6.2; other SGI configurations may also fail. Has to do with the namelist implementation; current work-around is to use a different machine(!)

  • The automated tests of Link, Edit, and Parm fail on DEC alpha machines, because of byte-ordering problems. This is a problem with the test suite, *not* with the programs themselves, which we believe are fine.

  • LINK does not generate dihedrals about a covalent bond generated with the ICONN=1 option with specification of NA0/NM0. Defining the bond as a crosslink with ICROSL=1 works ok.

  • EDIT places sugar hydrogens wrong for A DNA. One solution is to fix the coordinates by hand and load the correct coordinates in the PDB file. Or use leap, which places hydrogens correctly.

  • In the test suite, ANAL gives one wrong measurement on Crays for nucleic acid sugar pucker phase: 
            73c73
        <       5   10 - CYT         0.39     61.23
        ---
        >       5   10 - CYT         0.39    118.77
  • ANAL energy discrepancy

Department of Chemistry and Chemical Biology, 102 Hurtig Hall, 360 Huntington Ave., Boston, MA 02115
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Last modified: Tuesday, April 01, 2003