Re: [gmx-users] PDB and GRO files

[Mark Abraham]

Jim Kress wrote:
Try Openbabel.  


http://openbabel.org/wiki/Main_Page

It intercoverts most file types so, you could build your molecule with any
of the 3D model builders that serve as front ends to Quantum Chemistry
programs.  Export it as an XYZ file and then use Openbabel to convert it to
a pdb format.  Some will even export pdb formatted files.

For that matter, you could use ArgusLab to build your protein and/ or import
it from a known pdb file database.  If you choose to build your protein, it
will export it in a pdb format.  If you download one from a database,
obviously you can save it in a pdb format.

ArgusLab is also specifically designed to make building proteins simpler
(not simple - just simpler) with a built-in library of amino acids in
fragment forms that can be connected to create the protein of your choice
along with side chain fragments, solvation species, etc.

http://www.arguslab.com/

Highly recommended.


Wikified, thanks. 
http://oldwiki.gromacs.org/index.php/Coordinate_File#Sources


Mark
___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

RE: [gmx-users] PDB and GRO files

[Jim Kress]

Try Openbabel.  

http://openbabel.org/wiki/Main_Page

It intercoverts most file types so, you could build your molecule with any
of the 3D model builders that serve as front ends to Quantum Chemistry
programs.  Export it as an XYZ file and then use Openbabel to convert it to
a pdb format.  Some will even export pdb formatted files.

For that matter, you could use ArgusLab to build your protein and/ or import
it from a known pdb file database.  If you choose to build your protein, it
will export it in a pdb format.  If you download one from a database,
obviously you can save it in a pdb format.

ArgusLab is also specifically designed to make building proteins simpler
(not simple - just simpler) with a built-in library of amino acids in
fragment forms that can be connected to create the protein of your choice
along with side chain fragments, solvation species, etc.

http://www.arguslab.com/

Highly recommended.

Jim

> -Original Message-
> From: gmx-users-boun...@gromacs.org 
> [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul
> Sent: Tuesday, July 21, 2009 6:16 PM
> To: Gromacs Users' List
> Subject: Re: [gmx-users] PDB and GRO files
> 
> 
> 
> Jamie Seyed wrote:
> > Hi Justin,
> >  
> > On Tue, Jul 21, 2009 at 5:04 PM, Justin A. Lemkul  > <mailto: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 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
> >

Re: [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: 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 :


Hi Justin,

On Tue, Jul 21, 2009 at 5:04 PM, Justin A. Lemkul  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 > 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 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


   

Re: [gmx-users] PDB and GRO files

[Vitaly V. Chaban]

Yeah, we are friendly. :)

Don't hesitate to ask if you experience future problems.

~ Vitaly


On Wed, Jul 22, 2009 at 1:55 AM, Jamie Seyed  wrote:

> Thank you for your help and comments.
> -Jamie
>
>
>
>
___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] PDB and GRO files

[Justin A. Lemkul]

Jamie Seyed wrote:

Hi Justin,
 
On Tue, Jul 21, 2009 at 5:04 PM, Justin A. Lemkul > 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  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
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 


   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
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


   ___
   gmx-users mailing lis

Re: [gmx-users] PDB and GRO files

[Jamie Seyed]

Hi Justin,

On Tue, Jul 21, 2009 at 5:04 PM, Justin A. Lemkul  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 > 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 >> 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
>>
>>
>>___
>>gmx-users mailing listgmx-users@gromacs.org
>>
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at http://www.gromacs.org/search
>>before posting!
>>Please don't post (un)subscribe requests to the list. Use the
>>www interface or send it to gmx-users-requ...@gromacs.org
>>.
>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>
>>___
>>gmx-users mailing listgmx-users@gromacs.org
>>
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at http://www.gromacs.org/search before
>>posting!
>>Please don't post (un)subscribe requests to the list. Use the
>>www interface or send it to gmx-users-requ...@gromacs.org
>>.
>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>
>> 
>>
>> 

Re: [gmx-users] PDB and GRO files

[Justin A. Lemkul]

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 
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 
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 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


___
gmx-users mailing listgmx-users@gromacs.org

http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search
before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org
.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php



___
gmx-users mailing listgmx-users@gromacs.org

http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org
.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php





___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php


--


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


___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://ww

Re: [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_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
> 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 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
>>
>> ___
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
>
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] PDB and GRO files

[Rodrigo faccioli]

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  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
>
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] PDB and GRO files

[Jamie Seyed]

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
___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php