Hi,
Now when using the commands:
mods = loadAmoebaParams em_ac.frcmod
saveAmoebaParm mol prmtop inpcrd
I get the error:
get typeid of -1
sleap: data.cpp:424: bool mort::mcmpdata_t::get_iptr(const mort::hashid_t&,
int, const int*&) const: Assertion `absid >=0 && absid < m_idcounter'
failed.
Aborted
Any idea why saveAmoebaParm would cause this problem?
Thanks,
Rob
On Wed, Mar 30, 2011 at 10:43 AM, Ben Roberts <ben.roberts.geek.nz> wrote:
> Hi Rob,
>
> On 30/3/2011, at 9:12 a.m., r smith wrote:
>
> > Hello,
> >
> > I am using sleap in AmberTools version 1.4 to create prmtop and inpcrd
> files
> > for use with the amoeba force field. After loading the .mol2 file
> > em_ac.mol2 with the command:
> >
> > mol = loadmol2 em_ac.mol2
> >
> > I receive the following error:
> >
> > sleap: data.cpp:276: void mort::mcmpdata_t::set_s(const mort::hashid_t&,
> > int, const std::string&): Assertion `absid >= 0 && absid < m_idcounter'
> > failed.
> > Aborted
> >
> > However, the file is loaded without error when using tleap. I have
> attached
> > the .mol2 file. Do you notice anything in the file that would cause
> sleap
> > to fail?
>
> It would appear that the header of your mol2 file (the line between ACT and
> SMALL, that reads "29 28" etc.) specifies that your molecule contains only
> one residue - the third number on that line indicates the total number of
> residues expected (the first two numbers being the number of atoms, and the
> number of bonds). Atom records, however, refer to two separate residues (ACT
> and EMM).
>
> Changing that number from 1 to 2 makes the error go away.
>
> Hope this helps,
> Ben
>
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Received on Wed Mar 30 2011 - 09:30:04 PDT
