[gmx-users] PDB and GRO files

[Justin A. Lemkul]

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.

> 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 is the 
old home page.

-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>> 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/>
>     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>> 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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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