[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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