[gmx-users] Re: RMSD of the same protein in different solvent boxes
Afonso Duarte
duartenl at yahoo.com.br
Mon Feb 5 12:16:26 CET 2007
Thanks it worked!
I useed trjconv to create a new .xtc just with the backbone and now I can do a g_rms for both simulations.
Cheers
Afonso
Today's Topics:
1. Re: RMSD of the same protein in different solvent boxes
(Tsjerk Wassenaar)
2. Re: RMSD of the same protein in different solvent boxes
(Florian Haberl)
3. Re: RMSD of the same protein in different solvent boxes
(Ran Friedman)
----------------------------------------------------------------------
Message: 1
Date: Mon, 5 Feb 2007 11:22:23 +0100
From: "Tsjerk Wassenaar"
Subject: Re: [gmx-users] RMSD of the same protein in different solvent
boxes
To: "Discussion list for GROMACS users"
Message-ID:
<8ff898150702050222v5e26a791v74a4ebacdd62bae7 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi Afonso,
Try to first extract the protein from both simulations using trjconv,
or even the backbone trajectories.
Cheers,
Tsjerk
On 2/5/07, Afonso Duarte wrote:
> Hi to All,
>
> I have some simulations of the same protein in different solvents, with
> different number of atoms for each (different solvent number of atoms).
> I would like to calculate a rmsd matrix to compar the backbone of the
> different sims.
>
> I have tried g_rms with the -f2 option to include the second trajectory,
> however it finishes with a fatal error because teh number of total atoms is
> different in both trajectories.
>
> Does anybody know how to solve this question? Is it possible to produce the
> rmsd matrix in a different way?
>
> Thanks in advance
>
> Afonso
>
>
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--
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
------------------------------
Message: 2
Date: Mon, 5 Feb 2007 11:31:27 +0100
From: Florian Haberl
Subject: Re: [gmx-users] RMSD of the same protein in different solvent
boxes
To: Discussion list for GROMACS users
Message-ID: <200702051131.28088.Florian.Haberl at chemie.uni-erlangen.de>
Content-Type: text/plain; charset="utf-8"
hi,
On Monday, 5. February 2007 11:13, Afonso Duarte wrote:
> Hi to All,
>
> I have some simulations of the same protein in different solvents, with
> different number of atoms for each (different solvent number of atoms). I
> would like to calculate a rmsd matrix to compar the backbone of the
> different sims.
>
> I have tried g_rms with the -f2 option to include the second trajectory,
> however it finishes with a fatal error because teh number of total atoms is
> different in both trajectories.
>
> Does anybody know how to solve this question? Is it possible to produce the
> rmsd matrix in a different way?
reduce both simulations to matching atomsize, e.g. for both simulations:
make_ndx (only backbone atoms)
trjconv ..
g_rms
>
> Thanks in advance
>
> Afonso
>
> __________________________________________________
> Fale com seus amigos de graça com o novo Yahoo! Messenger
> http://br.messenger.yahoo.com/
greetings,
Florian
--
-------------------------------------------------------------------------------
Florian Haberl
Computer-Chemie-Centrum
Universitaet Erlangen/ Nuernberg
Naegelsbachstr 25
D-91052 Erlangen
Telephone: +49(0) − 9131 − 85 26581
Mailto: florian.haberl AT chemie.uni-erlangen.de
-------------------------------------------------------------------------------
------------------------------
Message: 3
Date: Mon, 05 Feb 2007 11:22:55 +0100
From: Ran Friedman
Subject: Re: [gmx-users] RMSD of the same protein in different solvent
boxes
To: Discussion list for GROMACS users
Message-ID: <45C7057F.6050600 at bioc.unizh.ch>
Content-Type: text/plain; charset="iso-8859-1"
Hi,
If it's the same protein you can extract the trajectories with the
coordinates of the protein only using trjconv.
Ran.
Afonso Duarte wrote:
> Hi to All,
>
> I have some simulations of the same protein in different solvents,
> with different number of atoms for each (different solvent number of
> atoms).
> I would like to calculate a rmsd matrix to compar the backbone of the
> different sims.
>
> I have tried g_rms with the -f2 option to include the second
> trajectory, however it finishes with a fatal error because teh number
> of total atoms is different in both trajectories.
>
> Does anybody know how to solve this question? Is it possible to
> produce the rmsd matrix in a different way?
>
> Thanks in advance
>
> Afonso
>
> __________________________________________________
> Fale com seus amigos de graça com o novo Yahoo! Messenger
> http://br.messenger.yahoo.com/
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> 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
--
------------------------------------------------------
Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355593
Email: r.friedman at bioc.unizh.ch
Skype: ran.friedman
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