[gmx-users] problem with trjconv

[OZGE ENGIN]

Hi,

First of all, thank you for your attention. I used g_hbond in order to analyze  hydrogen bonds formed;but, I need a more detailed information. The command that you mentioned is capable of giving information about hydrogen bonds formed in each frame. However, I want to investigate the exact donor and acceptor groups in each frame. In this respect, I converted the xtc file to a pdb file  to get all of the coordinates of both water and protein molecules.
What should I do?

Thanks in advance

Ozge

-----Original Message-----
From: "Tsjerk Wassenaar" <tsjerkw at gmail.com>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Wed, 28 Feb 2007 17:52:34 +0100
Subject: Re: [gmx-users] problem with trjconv

Hi Ozge,

Why do you first want to go to a .pdb trajectory? Gromacs comes with
g_hbond, which can analyze hydrogen bonds for you, as well as giving
you an index file containing the atoms involved in hydrogen bonds,
which you can use to extract those from your trajectory. In addition,
g_hbond also does "normal" contacts, other than hydrogen bonds.

Tsjerk

On 2/28/07, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> OZGE ENGIN wrote:
> > Hi,
> >
> > I have a problem with the trjconv command.
> >
> > I performed a 30 ns simulation, and wanted to analyze hydrogen bonds formed between protein and water molecules. In this respect, I converted the xtc file into a pdb file by selecting system option. As you can understand the overall file was such a large file that I could not handle it. So, I want to know whether there is any possibility to select water molecules within a cutoff value or to extract frames within  given time steps? For instance, at every 70 th step, from 70 ps to 80 ps.
>
> If you read the man page for trjconv, you will see an option to do the
> latter. I don't think the former is implemented in the gromacs utilities.
>
> Mark
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>


-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
_______________________________________________
gmx-users mailing list    gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php