Dear case,
I'd like to know if carbon atom "C" is the type for carbonyl carbon, not
aliphatic ones. What file should I check ?
thank you.
stwahyudi
On Mon, Aug 9, 2010 at 6:57 PM, case <case.biomaps.rutgers.edu> wrote:
> On Mon, Aug 09, 2010, setyanto tri wahyudi wrote:
>
> > I've been make prep file for hexane using Antechamber. After that, I make
> > force modifications using PARMCHK.
>
> Antechamber was primarily designed for use with the gaff force field. If
> you
> try to use other atom types (or your own), you will have often have
> lots of parameters to define yourself.
>
> It's not clear what command arguments you used, but your carbon atom (in
> hexane) is listed as "C", which doesn't make sense, since "C" is the type
> for
> a carbonyl carbon, not an aliphatic onse.
>
> > C -H 0.00 0.000 ATTN, need revision
>
> The "needs revision" statement means that parmchk doesn't know what
> parameters
> to put here, and you have to decide yourself. As stated above, try using
> gaff. If you don't like the suggested parameters, you can certainly change
> them, but gaff provides a good starting point.
>
> ....dac
>
>
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Received on Mon Aug 09 2010 - 20:30:03 PDT
