[gmx-users] PDB and GRO files

Rodrigo faccioli rodrigo_faccioli at uol.com.br
Tue Jul 21 22:17:34 CEST 2009


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.


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
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> 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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