Since it appears Amoeba may not recognize the atom types I'm using, what
files would need to be modified to add parameters to Amoeba?
Thanks,
Rob
On Wed, Mar 30, 2011 at 11:16 PM, Ben Roberts <ben.roberts.geek.nz> wrote:
>
> On 30/03/2011, at 9:52 PM, case wrote:
>
> > On Wed, Mar 30, 2011, Ben Roberts wrote:
> >>
> >> [gtkleap]$ saveAmoebaParm mol prmtop inpcrd
> >> saveAmoebaParm mol prmtop inpcrd
> >> get typeid of -1
> >> Error (get_iptr): while retrieving parameter typeid, impossible abs ID
> (-1)
> >
> > Note that amoeba (as implemented in Amber) is not a general force field.
> > I think it only works for proteins with standard residues. I suspect(!)
> > that this message is just a way of saying it doesn't have parameter types
> > for the atoms in your system. Do you think it should be able to
> recognize
> > everything?
>
> OK, I wasn't aware of that. I lose points for not doing the research, I
> guess.
>
> In which case, I can perhaps update the code so that it prints out a more
> informative message.
>
> Thanks,
> Ben
>
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Received on Wed May 04 2011 - 06:30:02 PDT
