On Mon, Sep 05, 2011, Danny Xu wrote:
>
> I tried to assign am1bcc charge to the attached mol2 file
> using antechamber. Sqm calculation finished just fine (sqm.out
> is also attached). However, antechamber failed to create
> ANTECHAMBER_AM1BCC_PRE.AC file and no error was printed out. The
> molecule has 156 atoms, below MAXATOM=256 defined for antechamber. I'd
> really appreciate if anyone can help pin down the problem.
First, this is not the way antechamber should be used. You should break
the molecule into small fragments, and determine the best charges for
each.
Second, the amino end group you have is deprotonated...that would probably
happen only at very high pH.
Third, atoms within a residue (or giant molecule in your case) should have
unique names. You have many, many atoms named "C1" etc. Antechamber tries to
fix things like this, but may fail.
....dac
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Received on Sun Sep 11 2011 - 19:00:02 PDT
