[gmx-users] PDB and GRO files
Justin A. Lemkul
jalemkul at vt.edu
Wed Jul 22 00:16:03 CEST 2009
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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> --
> ========================================
>
> 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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