[gmx-users] Warning _mesage

[Devika N T]

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+'

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

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







 * Regards**
  N.T. Devika*


On Wed, Jan 16, 2013 at 5:54 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==============================**==========
>
> 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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