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: jalem...@vt.edu
> To: gmx-users@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
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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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