[gmx-users] file.itp for separated molecules

[Justin A. Lemkul]

Fahimeh Baftizadeh wrote:
> 
> 
>     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?

Yes, pdb2gmx will write topologies for whatever molecules it finds (and 
obviously has .rtp entries for).

>     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?
> 

Yes.

>     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?!
> 

This is completely normal output.  Please see the manual, section 5.4 and the 
footnotes of Table 5.4 for the specifics of the nrexcl value.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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