[gmx-users] genbox
Justin A. Lemkul
jalemkul at vt.edu
Wed Apr 21 14:31:11 CEST 2010
shahid nayeem wrote:
> I was also trying to put more than one protein in one simulation box. I
> was able to do it with genconf but it appears that the addition is in
> very ordered manner if one looks .gro file in VMD. How can I add these
> protein in disordered random orientation.
That's certainly what genconf does. You can apply a random rotation to your
molecules with genconf -rot, but I don't know if that will remove any of the
regularity in overall position.
-Justin
> msnayeem
>
>
> On 4/20/10, *Justin A. Lemkul* <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> 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 <mailto:jalemkul at vt.edu>
> > To: gmx-users at gromacs.org <mailto: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 <mailto:jalemkul at vt.edu>
> > > > To: gmx-users at gromacs.org <mailto: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 <http://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 <http://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 <http://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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