VMD-L Mailing List

From: Sasha Buzko (obuzko_at_ucla.edu)
Date: Thu Apr 30 2009 - 16:38:51 CDT

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
>>
>>
>
>