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.
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.
-Justin
Thanks for your help,
Jamie
On Tue, Jul 21, 2009 at 4:17 PM, Rodrigo faccioli
<[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/>
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]>> 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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