[gmx-users] Warning _mesage

[Justin Lemkul]

On 1/16/13 7:38 AM, Devika N T wrote:
> Thank you Justin for your reply.
>
> I need to perform the effect of Calcium (CA) with protein Calmodulin.
>>From the warning message its clear that "CA" is not identified as ion.
> But previously I tried the run with Gromacs version 4.0.7 at that time
>
> Version 4.0.7
>
>
> Warning: 'CA' not found in residue topology database, trying to use 'CA2+'
> Warning: 'CA' not found in residue topology database, trying to use 'CA2+'
> Warning: 'CA' not found in residue topology database, trying to use 'CA2+'
> Warning: 'CA' not found in residue topology database, trying to use 'CA2+'
>

This only implies that the name is wrong with respect to what the .rtp file expects.

> So I thought in version 4.5.5 it will have the residuetype.dat file updated
> with calcium.
> Fine let me try by adding calcium to residuetypes.dat
>

That should be the solution.

> Anyway I cannot consider "calcium ion" as ligand right?
>

You can consider it however you like, but if you're interpreting a ligand to be 
something for which you need a topology from an external source, then no.  All 
Gromacs force fields have parameters for calcium and should be processed 
automatically by pdb2gmx.  In fact, I just checked residuetypes.dat and there is 
a line indicating CA as an Ion, so there should be no problem at all.  Looking 
more closely at the pdb2gmx output from your original post, all that is 
indicating is that there is a species that is not Protein/DNA/RNA, which in this 
case is of course what one would expect.  There is no problem whatsoever.

-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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