[gmx-users] genbox

[Justin A. Lemkul]

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

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