RE: [gmx-users] PDB and GRO files
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 jalem...@vt.edu 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 On Tue, Jul 21, 2009 at 4:17 PM, Rodrigo faccioli rodrigo_facci...@uol.com.br mailto:rodrigo_facci...@uol.com.br mailto: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
Re: [gmx-users] PDB and GRO files
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
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 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
Re: [gmx-users] PDB and GRO files
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 jamie.se...@gmail.comwrote: 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
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 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 ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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 mailto: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
Re: [gmx-users] PDB and GRO files
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 ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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 mailto: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
Re: [gmx-users] PDB and GRO files
Jamie Seyed wrote: Hi Justin, On Tue, Jul 21, 2009 at 5:04 PM, Justin A. Lemkul jalem...@vt.edu 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 On Tue, Jul 21, 2009 at 4:17 PM, Rodrigo faccioli rodrigo_facci...@uol.com.br mailto:rodrigo_facci...@uol.com.br mailto: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/ 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 mailto: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
Re: [gmx-users] PDB and GRO files
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 jamie.se...@gmail.com 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
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,
