Jamie Seyed wrote:
Hi Justin,
On Tue, Jul 21, 2009 at 5:04 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> 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 documentation of each program will explain the output formats.
The systems that I want to simulate are fullerene and CNT. But before
Then neither PRODRG nor xLeap will be of use to you; xLeap might work, but it's
probably about the hardest way to do it :)
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?
Use spc216.gro - it's a pre-equilibrated box that is suitable for use in further
simulations.
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 <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"...
Use Google to search for PRODRG; the link in the wiki article is incorrect. But
as I said above, for your purposes, PRODRG is not useful.
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 (?).
Use Google to find things.
This page is probably where you will want to start:
http://www.gromacs.org/WIKI-import/Carbon_Nanotube
-Justin
Thanks a lot,
Jamie
-Justin
Thanks for your help,
Jamie
On Tue, Jul 21, 2009 at 4:17 PM, Rodrigo faccioli
<[email protected]
<mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>>> 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/>
<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
<[email protected] <mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>>> 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 <http://vt.edu/> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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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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