[gmx-users] Warning _mesage

[Devika N T]

Thank you Justin for your valuable suggestion.
I will follow it up.








 * Regards**
  N.T. Devika*


On Wed, Jan 16, 2013 at 6:16 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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