[gmx-users] Warning _mesage

[Justin Lemkul]

On 1/16/13 5:32 AM, Devika N T wrote:
> 4.5.5 versio
>
> Writing topology
> Processing chain 2 'A' (4 atoms, 4 residues)
> Warning: Starting residue CA149 in chain not identified as Protein/RNA/DNA.
> Warning: Starting residue CA150 in chain not identified as Protein/RNA/DNA.
> Warning: Starting residue CA151 in chain not identified as Protein/RNA/DNA.
> Warning: Starting residue CA152 in chain not identified as Protein/RNA/DNA.
> Problem with chain definition, or missing terminal residues.
> This chain does not appear to contain a recognized chain molecule.

Note what the following line tells you:

> If this is incorrect, you can edit residuetypes.dat to modify the behavior.
>
>

So pdb2gmx is recognizing "CA" (calcium?) as some unknown type.  This may or may 
not be relevant for your purposes.  The topology should have been written just 
fine as long as the parent force field recognizes CA.  If it is an ion, do as 
pdb2gmx suggests and add this information to residuetypes.dat, which will make 
default group generation easier later on.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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