[gmx-users] genbox

[fahimeh bafti]

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

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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