On Tue, Jan 05, 2010, Mark M Huntress wrote:
>
> antechamber -i retch.pdb -fi pdb -o retch.mol2 -fo mol2 -c bcc
>
> The error was:
>
> 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 MAXVASTATE in define.h and recompile bondtype.C
> (4) increase PSCUTOFF in define.h and recompile bondtype.C
>
> > Hi, I am trying to parameterize a molecule (protonated, positively
> > charged retinal) and I am getting the following error when I put in the
> > following input:
Since your molecule is a cation, you have to include the "-nc 1" flag
to tell antechamber that this is an ion; by default it assumes that the
molecule has no net charge. Also, when you have problems with the default
"-j 4" flag, it is often good to try "-j 5". Hence for me, the command:
antechamber -i retch.pdb -fi pdb -o retch.mol2 -fo mol2 -c bcc -nc 1 -j 5
gives a reasonable-looking mol2 file. (Be sure to check for yourself:
antechamber results, especially for polyenes, should be viewed as a good first
step, not as gospel. It doesn't know about fractional bond orders, but those
are not used by Amber anyway. However, torsional barriers to rotation
predicted by GAFF for a highly delocalized system like this one are unlikely
to be reliable; I don't know if this is important for what you want to do or
not.)
...hope this helps...dac
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Received on Tue Jan 05 2010 - 21:00:04 PST
