From: Sasha Buzko (obuzko_at_ucla.edu)
Date: Thu Apr 30 2009 - 16:13:41 CDT

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