[gmx-users] Editing of the existing system

[Mark Abraham]

On 31/03/2012 1:00 AM, James Starlight wrote:
> Mark,
>
>
> Also I'd like to know some more about most correct parametrisation of 
> such new edited system. My new system consist of two proteins ( one- 
> wich was initially and the second small peptide wich I've docked to 
> the first protein). So now I need to define 2 separate groups for the 
> below enties of my MD files
>
> |energygrps = Protein peptide
> |
> tc-grps     = Protein_Bilayer SOL_ions_peptide
>
> and finally CoM groups because of the general anisotropy of the membrane system
>
>
> comm-grps	= Protein_Bilayer SOL_Ions_Peptide
>
> I've made itp file for the peptide via pdb2gmx so in th default definition both the protein and peptide are the protein enty in the index file.
>
> I've separate both of the protein and peptide by selection of two subsets of atoms wich represent to the each of that enties.
>
>
> So finally I have two groups in the index.ndx file
>
> a_1-5000  ( it's protein)
> a_9999-10500 (it's peptide)

You can use make_ndx (or a text editor on the .ndx file) to give them 
more helpful names.

> Does this separation correct in general ? I have some fears because both protein and peptide consist of the same residue numbers in the GRO file ( e.g there are 212- lys wich is part of the protein and 212-Pro wich is part of the peptide ) Might this system be tended to errors?

Residue numbers are largely irrelevant. pdb2gmx and maybe grompp use 
them for matching a coordinate file to the .rtp and .top (respectively), 
but only really in the sense that the number changes from one residue to 
another.

> I have no errors during processing of that sustem by grompp as well as md run. What should I do for such system consisted of two proteins in separate phases ( membrane-like and water)
> ?

All seems basically sound.

Mark
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