From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Apr 30 2009 - 16:52:18 CDT

Please try without including the par_ file, which is a parameter file
and probably gave errors when you tried to read it. I should have noted
that explicitly; in charmm one would load both the topology and
parameter files, but for psfgen/autopsf you only want the topology file.
Peter

Sasha Buzko wrote:
> Thank you, Peter.
> Surprisingly enough, I now get "unknown residue type ATP".
>
> The files added in the Topology box:
> top_all27_prot_lipid.inp
> top_all27_na.rtf
> par_all27_na.prm
> toppar_all27_na_nad_ppi.str
>
> The source PDB residue/atom naming is still consistent with the
> parameter files.. The first file (top_all27_prot_lipid.inp) wasn't part
> of the bundled distribution, but came from another site. It worked fine
> on kinase alone, though..
>
> Sasha
>
>
> Peter Freddolino wrote:
>> 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
>>>
>>>
>>
>>