[gmx-users] PDB and GRO files
Jim Kress
jimkress_58 at kressworks.org
Fri Jul 24 23:27:40 CEST 2009
Try Openbabel.
http://openbabel.org/wiki/Main_Page
It intercoverts most file types so, you could build your molecule with any
of the 3D model builders that serve as front ends to Quantum Chemistry
programs. Export it as an XYZ file and then use Openbabel to convert it to
a pdb format. Some will even export pdb formatted files.
For that matter, you could use ArgusLab to build your protein and/ or import
it from a known pdb file database. If you choose to build your protein, it
will export it in a pdb format. If you download one from a database,
obviously you can save it in a pdb format.
ArgusLab is also specifically designed to make building proteins simpler
(not simple - just simpler) with a built-in library of amino acids in
fragment forms that can be connected to create the protein of your choice
along with side chain fragments, solvation species, etc.
http://www.arguslab.com/
Highly recommended.
Jim
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org
> [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul
> Sent: Tuesday, July 21, 2009 6:16 PM
> To: Gromacs Users' List
> Subject: Re: [gmx-users] PDB and GRO files
>
>
>
> Jamie Seyed wrote:
> > Hi Justin,
> >
> > On Tue, Jul 21, 2009 at 5:04 PM, Justin A. Lemkul <jalemkul at vt.edu
> > <mailto:jalemkul at vt.edu>> wrote:
> >
> >
> >
> > Jamie Seyed wrote:
> >
> > Hi,
> > Thanks for your comments. But I do not know how to
> get (or make)
> > the pdb file if it is not made (let say for a new
> system). Are
> > you using special software to do that to make a pdb
> or gro file,
> > before starting the simulation?
> >
> >
> > That's going to depend entirely upon what that system
> is. Building
> > a protein or peptide is not so trivial. Building a
> small molecule
> > is fairly straightforward using programs like PRODRG (online) or
> > xLeap (part of AmberTools).
> >
> > That said, if your goal is to simulate some arbitrary small
> > molecules, the previous advice of using pdb2gmx will
> not apply. You
> > will have to build the topologies yourself.
> >
> >
> > Is the result of using these programs a pdb file or gro...... would
> > you please explain a little bit?
>
> The documentation of each program will explain the output formats.
>
> > The systems that I want to simulate are fullerene and CNT.
> But before
>
> Then neither PRODRG nor xLeap will be of use to you; xLeap
> might work, but it's probably about the hardest way to do it :)
>
> > that I will simulate a box of water, spce. In this case is it ok to
> > use spc216.pdb (??) or I should use the programs you mentioned?
>
> Use spc216.gro - it's a pre-equilibrated box that is suitable
> for use in further simulations.
>
> > Sorry for these simple questions......
> >
> >
> >
> > Another thing: It is not possible for me to open
> some web-pages
> > that users are referring to (some of them are
> crucial to get the
> > answer)!! Did you face with the same problem or there is new
> > web-address for them??
> >
> >
> >
> > If you cite some examples, maybe someone can point you
> in the right
> > direction. The Gromacs webpage is currently migrating
> to a new site;
> > old webpages can be accessed by appending "old" to the URL, i.e.
> > http://oldwww.gromacs.org <http://oldwww.gromacs.org/>
> is the old
> > home page.
> >
> >
> > For example I checked
> http://www.gromacs.org/WIKI-import/PRODRG as you
> > mentioned, but I can not open links on the page. All of them (check
> > force field for example) can not open with like this message "Site
> > settings could not be loaded"...
>
> Use Google to search for PRODRG; the link in the wiki article
> is incorrect. But as I said above, for your purposes, PRODRG
> is not useful.
>
> > Is it the page I should use to get a pdb file for my
> system?? I really
> > appreciate if you let me know the exact web-address to use
> PRODRG or
> > xLeap (?).
> >
>
> Use Google to find things.
>
> This page is probably where you will want to start:
>
> http://www.gromacs.org/WIKI-import/Carbon_Nanotube
>
> -Justin
>
> > Thanks a lot,
> > Jamie
> >
> >
> >
> >
> > -Justin
> >
> > Thanks for your help,
> > Jamie
> >
> > On Tue, Jul 21, 2009 at 4:17 PM, Rodrigo faccioli
> > <rodrigo_faccioli at uol.com.br
> > <mailto:rodrigo_faccioli at uol.com.br>
> > <mailto:rodrigo_faccioli at uol.com.br
> > <mailto:rodrigo_faccioli at uol.com.br>>> wrote:
> >
> > Hi,
> >
> > If I understood your question, do you want to
> know how can
> > you start
> > a simulation? So, if I'm correct I recommend this link
> >
> http://www.gromacs.org/WIKI-import/Main_Page/Beginners to you. In
> > this link, there is flowsheet file which is the
> flowchart to
> > Gromacs
> > simulation.
> >
> > Answered your question a little more specific, although
> > basically, after you get the pdb file, you need
> to run the
> > pdb2gmx program. The
> > link above explains more details about it.
> >
> > I hope that this email helped you.
> >
> > Cheers,
> > --
> > Rodrigo Antonio Faccioli
> > Ph.D Student in Electrical Engineering
> > University of Sao Paulo - USP
> > Engineering School of Sao Carlos - EESC
> > Department of Electrical Engineering - SEL
> > Intelligent System in Structure Bioinformatics
> > http://laips.sel.eesc.usp.br
> <http://laips.sel.eesc.usp.br/>
> > <http://laips.sel.eesc.usp.br/>
> >
> > Phone: 55 (16) 3373-9366 Ext 229
> > Curriculum Lattes -
> http://lattes.cnpq.br/1025157978990218
> >
> >
> > On Tue, Jul 21, 2009 at 4:52 PM, Jamie Seyed
> > <jamie.seyed at gmail.com <mailto:jamie.seyed at gmail.com>
> > <mailto:jamie.seyed at gmail.com
> > <mailto:jamie.seyed at gmail.com>>> wrote:
> >
> > Hi,
> >
> > I have a basic question (since I am new).
> For starting any
> > simulation as I understand, is to find a .pdb or .gor
> > file. Pdb
> > files for proteins are already there, but for a new
> > system what
> > is the easiest and quick way to find it
> (which software etc).
> > What about .gro files?????
> >
> >
> > I appreciate your help for solve my basic problems.
> >
> > Thanks, Jamie
> >
> >
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> ----------------------------------------------------------------------
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> >
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> >
> > --
> > ========================================
> >
> > Justin A. Lemkul
> > Ph.D. Candidate
> > ICTAS Doctoral Scholar
> > 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
> 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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