[gmx-users] genbox

[Justin A. Lemkul]

fahimeh bafti wrote:
> Thanks :)
> but I couldn't manage with that, it makes the same error with editconf 
> as well, the problem was related to having more than one residue inside 
> insert.gro

editconf should not have a problem placing multi-residue molecules within a box. 
  That is its main function, so I can only assume you did something wrong.

> I did it at the end with genconf
> 
> genconf  -nbox 2 2 2 (as u want)  -f  file.gro  -o file_replicate.pdb
> 
> it will simply replicate the unit.
> 

That works.  Glad you found a solution.

-Justin

> Fahimeh
> 
>  > Date: Tue, 20 Apr 2010 09:12:44 -0400
>  > From: jalemkul at vt.edu
>  > To: gmx-users at gromacs.org
>  > Subject: Re: [gmx-users] genbox
>  >
>  >
>  >
>  > fahimeh bafti wrote:
>  > > Thank you Justin
>  > > but I end up with a new error. now in the insert.pdp file I have a
>  > > molecule which I need to add 4 copy of that inside the solute.pdb
>  > > genbox_d -ci insert.pdb -nmol 4 -cp solute.pdb
>  > >
>  > > but it gave me:
>  > >
>  > > Fatal error:
>  > > more then one residue in insert molecules
>  > > program terminated
>  > >
>  >
>  > Then you have two options:
>  >
>  > 1. Use the development (git) version of the code, which I believe can 
> now deal
>  > with multi-residue molecules.
>  > 2. Use editconf to position all the components of your system.
>  >
>  > You could, I suppose, hack your "insert.pdb" to contain one residue 
> (i.e.,
>  > through renaming and renumbering) and then convert it back, but that 
> sounds like
>  > a mess. Probably #2 is the easiest.
>  >
>  > -Justin
>  >
>  > > Fahimeh
>  > >
>  > >
>  > > > Date: Tue, 20 Apr 2010 07:10:59 -0400
>  > > > From: jalemkul at vt.edu
>  > > > To: gmx-users at gromacs.org
>  > > > Subject: Re: [gmx-users] genbox
>  > > >
>  > > >
>  > > >
>  > > > fahimeh bafti
>  > > > > Hello,
>  > > > >
>  > > > > I want to use a file.pdb which has 8 chain of polypeptide, each 
> chain
>  > > > > contains 6 residues. I need to expand it to 12 chains of 6 rsidues
>  > > so I
>  > > > > need to add 4 chains or in the other word 24 residues. I think I
>  > > have to
>  > > > > use genbox, so I make another copy of file.pdb and rename it to
>  > > > > insert.pdb and i used this command, but it doesn't work.
>  > > > >
>  > > > > genbox -cp file.pdb -ci insert.pdb -nmole 24 -o out.gro
>  > > > >
>  > > > > can anybody help me?
>  > > >
>  > > > The implication with genbox -ci -nmol is that the coordinate file
>  > > passed to -ci
>  > > > contains one molecule, and an additional -nmol molecules are
>  > > inserted. So if
>  > > > you already have 8, you need a coordinate file with one polypeptide
>  > > and then:
>  > > >
>  > > > genbox -ci insert.pdb -nmol 4
>  > > >
>  > > > Note in the documentation that -nmol refers to the number of
>  > > molecules, not a
>  > > > number of residues, which I think is the root of your problem.
>  > > >
>  > > > -Justin
>  > > >
>  > > > >
>  > > > > Fahimeh
>  > > > >
>  > > > >
>  > > 
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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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>  > --
>  > ========================================
>  >
>  > 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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-- 
========================================

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

========================================