From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Apr 30 2009 - 16:30:30 CDT

Hi Sasha,
as noted in the comments at the top of the stream file that you are
including, you also need to read top_all27_na.rtf in order yo use that
stream file.
Peter

Sasha Buzko wrote:
> Hi,
> I'm trying to use NAMD to run MD of a protein with bound GTP and a
> magnesium ion, in order to compare to my prior Amber simulations. But
> since the GTP/Mg setup has so far failed miserably, I'm taking smaller
> steps. So at this point, it's a protein kinase with ATP bound.
>
> When running GUI of autopfs with the protein-ATP complex, chain
> generation fails ("failed at end of segment"). Tk console shows the
> error as "unknown atom type ON3". It refers to one of the phosphate
> oxygens in the ATP, according to the toppar file.
>
> I'm using VMD 1.8.6 and top_all27_prot_lipid.inp. As the source of the
> ATP parameters, I'm loading toppar_all27_na_nad_ppi.str from the
> toppar_c35b2_c36a2 distribution. I checked atom/residue naming between
> the parameter file and the PDB source, and they are identical.
>
> Could anyone suggest a possible source of this error?
>
> Thanks in advance for any suggestions
>
> Sasha
>