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* <[email protected]
<mailto:[email protected]>> 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: [email protected] <mailto:[email protected]>
> To: [email protected] <mailto:[email protected]>
> 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: [email protected] <mailto:[email protected]>
> > > To: [email protected] <mailto:[email protected]>
> > > 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
> > > 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
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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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Ph.D. Candidate
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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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