[gmx-users] genbox

[fahimeh bafti]

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
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.

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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> >  > --
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> >  > Justin A. Lemkul
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> >  > Department of Biochemistry
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> >  > Blacksburg, VA
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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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