[gmx-users] PDB and GRO files

[Alexandre Suman de Araujo]

Hi Jamie.

Another (free)options to generate the coordinate files (pdb or gro, they are
basically the same and can be converted into another using the trjconv tool)
are Molden and VMD.

With Molden you can build a molecule from scratch easily. I recommend it to
draw
small molecules like drugs.

VMD (version 1.8.7) has two tools that can be what you are looking for. With
Molefacture plugin you can draw small molecules and peptides. With Nanotube
Builder plugin you can easily build the CNTs you are interested. To construct
fullerenes I don't konw any VMD plugin, but probably somebody has already done
some plugin or script to generate this kind of molecules, try to search in
google by "fullerenes and VMD"

Cheers


-- 
**************************************************************
Alexandre Suman de Araujo                                    *
Faculdade de Ciências Farmacêuticas de Ribeirão Preto        *
Universidade de São Paulo                                    *
Dep. de Física e Química                                     *
Grupo de Física Biológica     * e-mail: asaraujo at fcfrp.usp.br*
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**************************************************************


Quoting Jamie Seyed <jamie.seyed at gmail.com>:

> Hi Justin,
>
> On Tue, Jul 21, 2009 at 5:04 PM, Justin A. Lemkul <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 systems that I want to simulate are fullerene and CNT. But before 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?
> 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 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"...
> 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
> (?).
>
> 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>> 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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>



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