On Wed, Nov 02, 2011, Matthew D Antalek wrote:
>
> When I try to create the prepin file I get the following error.
>
> [matthew.matt-pc octMD]$ antechamber -i short_taxolderivnoH.pdb -fi pdb -o
> s_tdnH.prepin -fo prepi -c bcc -s 2
> Running: /home/matthew/amber11/bin/bondtype -j full -i
> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
>
> Warning: the assigned bond types may be wrong, please :
> (1) double check the structure (the connectivity) and/or
> (2) adjust atom valence penalty parameters in APS.DAT, and/or
> (3) increase PSCUTOFF in define.h and recompile bondtype.c
> Be cautious, use a large value of PSCUTOFF (>100) will significantly
> increase the computation time
>
> Is this an error from an incorrect compilation of antechamber.c or is it
> because there are some default values in APS.DAT or bondtype.c file which
> are poor or incompatible with the molecule?
It's almost always becasue your input PDB file is bad, although the error
message should be clearer about that. The first instruction, "double check
the structure" is what you need to do. Options (2) and (3) are so arcane
that they should probably not even be mentioned.
Your filename is quite suspicous: "short_taxolderivnoH.pdb": input files to
antechamber must have all hydrogens present. sleap has a "fastbld" option
which often does the trick, but be sure to check its results visually. You
may just want to add the hydrogens by hand using your favorite molecular
builder.
...good luck....dac
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Received on Wed Nov 02 2011 - 19:00:04 PDT
