[gmx-users] file.itp for separated molecules

[Fahimeh Baftizadeh]

Hello
>
> I have to question.
> 1- I am generating a gro and toplogy file from a pdb file, usign pdb2gmx.
> the pdb file contains 18 separate chains, in each chain, there are 6
> residues.
> When I generate the topology and coordinates, it creates 18
> posres-protein$i.itp file and 18 topol-protein$i.itp file and then one
> topol.top and one conf.gro ...
>
> is it normal?
> i think it is just the position restraint for separate chains ... in this
> way i think it enables me to restraint them separately if i want? right?
>
> 2- using topol.top and conf.gro, after solvating the molecule in the box
> of water ... with editconf and genbox ... I am trying to generate a tpr
> file, but when it generate it writes the following:
>
> Generated 2211 of the 2211 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 2211 of the 2211 1-4 parameter combinations
> Excluding 3 bonded neighbours molecule type 'Protein'
> Excluding 3 bonded neighbours molecule type 'Protein2'
> Excluding 3 bonded neighbours molecule type 'Protein3'
> Excluding 3 bonded neighbours molecule type 'Protein4'
> Excluding 3 bonded neighbours molecule type 'Protein5'
> Excluding 3 bonded neighbours molecule type 'Protein6'
> Excluding 3 bonded neighbours molecule type 'Protein7'
> Excluding 3 bonded neighbours molecule type 'Protein8'
> Excluding 3 bonded neighbours molecule type 'Protein9'
> Excluding 3 bonded neighbours molecule type 'Protein10'
> Excluding 3 bonded neighbours molecule type 'Protein11'
> Excluding 3 bonded neighbours molecule type 'Protein12'
> Excluding 3 bonded neighbours molecule type 'Protein13'
> Excluding 3 bonded neighbours molecule type 'Protein14'
> Excluding 3 bonded neighbours molecule type 'Protein15'
> Excluding 3 bonded neighbours molecule type 'Protein16'
> Excluding 3 bonded neighbours molecule type 'Protein17'
> Excluding 3 bonded neighbours molecule type 'Protein18'
> Excluding 2 bonded neighbours molecule type 'SOL'
>
> what is this telling me? I didn't find a solution searching in the mailing
> list?!
>
> Thanks
> Fahimeh
>
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