[gmx-users] PDB and GRO files

[Jamie Seyed]

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?
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??

Thanks for your help,
Jamie

On Tue, Jul 21, 2009 at 4:17 PM, Rodrigo faccioli <
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
> 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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>
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