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: asara...@fcfrp.usp.br*
Av. do Café, s/n° * e-mail: ale.su...@gmail.com *
CEP: 14040-903 * Phone: +55 (16) 3602-4172 *
Ribeirão Preto, SP, Brasil * Phone: +55 (16) 3602-4222 *
**************************************************************
Quoting Jamie Seyed <jamie.se...@gmail.com>:
Hi Justin,
On Tue, Jul 21, 2009 at 5:04 PM, Justin A. Lemkul <jalem...@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_facci...@uol.com.br <mailto:rodrigo_facci...@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.se...@gmail.com
<mailto:jamie.se...@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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