[gmx-users] RE: gmx-users Digest, Vol 47, Issue 58
Evanildo Júnior
evanildojunior at hotmail.com
Tue Mar 18 21:12:56 CET 2008
> From: gmx-users-request at gromacs.org
> Subject: gmx-users Digest, Vol 47, Issue 58
> To: gmx-users at gromacs.org
> Date: Tue, 18 Mar 2008 12:00:06 +0100
>
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> Today's Topics:
>
> 1. RE: average structure with ligand (#NGUYEN CONG TRI#)
> 2. Re: average structure with ligand (Ran Friedman)
> 3. RE: Force field (?ngel Pi?eiro)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 18 Mar 2008 17:15:42 +0800
> From: "#NGUYEN CONG TRI#" <NGUY0045 at ntu.edu.sg>
> Subject: RE: [gmx-users] average structure with ligand
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Message-ID:
> <E476542CD98D094999A0FF7E022A465C013B1A57 at MAIL23.student.main.ntu.edu.sg>
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Anna,
>
> I think you can use make_ndx to make a new group for your ligand+protein. For example:
> $make_ndx -f filename.gro -o filename.ndx
> It will list all of the groups in you filename.gro file. Then select your protein and ligand and make a new name for the group. Use your filename.ndx index file as input to g_rmsf together with other files.
> Hope this can help.
>
> Regards,
> Tri.
>
> ________________________________
>
> From: gmx-users-bounces at gromacs.org on behalf of Anna Marabotti
> Sent: Tue 3/18/2008 4:47 PM
> To: gmx-users at gromacs.org
> Subject: [gmx-users] average structure with ligand
>
>
>
> Dear gmx-users,
> I would like to create from my trajectory an average structure of my protein with its ligand inside.
> With both g_rmsf and g_cluster I am prompted to indicate one group, but ligand and protein are
> separated into different groups, and I'd want to exclude water from this structure, so I don't want
> to indicate "system". I checked into the mailing list but didn't find any suggestion. Does anybody
> has one?
> Many thanks in advance and regards
> Anna Marabotti
>
> ______________________________________________
> Anna Marabotti, Ph.D.
> Laboratorio di Bioinformatica e Biologia Computazionale
> Istituto di Scienze dell'Alimentazione, CNR
> Via Roma 52 A/C
> 83100 Avellino (Italy)
> Tel: +39 0825 299651
> Fax: +39 0825 781585
> Skype: annam1972
> E-mail: amarabotti at isa.cnr.it
> Web page: http://bioinformatica.isa.cnr.it/anna.htm
> ____________________________________________________
> "If you think you are too small to make a difference, try sleeping with a mosquito"
>
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> ------------------------------
>
> Message: 2
> Date: Tue, 18 Mar 2008 10:16:01 +0100
> From: Ran Friedman <r.friedman at bioc.uzh.ch>
> Subject: Re: [gmx-users] average structure with ligand
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <47DF8851.4030805 at bioc.uzh.ch>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dear Anna,
>
> Use make_ndx to create any group you find useful.
>
> Ran.
>
> Anna Marabotti wrote:
> > Dear gmx-users,
> > I would like to create from my trajectory an average structure of my protein with its ligand inside.
> > With both g_rmsf and g_cluster I am prompted to indicate one group, but ligand and protein are
> > separated into different groups, and I'd want to exclude water from this structure, so I don't want
> > to indicate "system". I checked into the mailing list but didn't find any suggestion. Does anybody
> > has one?
> > Many thanks in advance and regards
> > Anna Marabotti
> >
> > ______________________________________________
> > Anna Marabotti, Ph.D.
> > Laboratorio di Bioinformatica e Biologia Computazionale
> > Istituto di Scienze dell'Alimentazione, CNR
> > Via Roma 52 A/C
> > 83100 Avellino (Italy)
> > Tel: +39 0825 299651
> > Fax: +39 0825 781585
> > Skype: annam1972
> > E-mail: amarabotti at isa.cnr.it
> > Web page: http://bioinformatica.isa.cnr.it/anna.htm
> > ____________________________________________________
> > "If you think you are too small to make a difference, try sleeping with a mosquito"
> >
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.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-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
> ------------------------------------------------------
>
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 18 Mar 2008 10:38:29 +0100
> From: ?ngel Pi?eiro <fangel at usc.es>
> Subject: RE: [gmx-users] Force field
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <1205833109.31216.65.camel at lysine>
> Content-Type: text/plain; charset=utf-8
>
> Hi Nihar,
> unfortunately I can't help you with thioflavin parameterization and
> probably other people here will address you to general links. Our CDs
> were built on the base of topologies for smaller sugars already
> available in the gromos force field (pasting building blocks). I hope
> someone else can help you with thioflavin...
>
> Regards,
>
> Angel.
>
>
> On Tue, 2008-03-18 at 10:11 +0530, Dr. Niharendu Choudhury wrote:
> > Hi �ngel,
> > Thanks a lot for coming forward. Regarding CD (\alpha, \beta and \gamma) I
> > will contact you as soon as possible. For the moment I would like to get
> > the same for Thioflavin-T. It is a fairly big molecules with I think 39
> > atoms. Can you tell me how go about (procedure in detail) to get the FF
> > from QM calculation?
> >
> > I must thank you again.
> >
> > Nihar
> >
> > Quoting �ngel Piñeiro <fangel at usc.es>:
> >
> > > Dear Nihar,
> > > if you contact me off the list I could send to you itp files for native
> > > alpha, beta, and gamma cyclodextrins compatible with the gromos forcefield
> > > (the ones we used in "jpcb (2007) 4383" and "jpcb (2007) 12625").
> > > Unfortunately I do not have the thioflavin.
> > >
> > > Regards,
> > >
> > > Angel Piñeiro.
> > >
> > >
> > > -----Mensaje original-----
> > > De: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] En
> > > nombre de Dr. Niharendu Choudhury
> > > Enviado el: sábado, 15 de marzo de 2008 02:54 a.m.
> > > Para: Discussion list for GROMACS users
> > > Asunto: [gmx-users] Force field
> > >
> > > Hi GROMACS users,
> > > I would like to study cyclodextrin + Thioflavin T in water. Is there any
> > > forcefiled parameters for these in any of the force-field supplied with
> > > GROMACS?
> > >
> > > It will be extremely beneficial if anybody can supply field compatible with
> > > GROMACS OR force-field parameters for CHARMM like potential functions.
> > >
> > > Sincerely
> > > Nihar
> > >
> > > *************************************************************************
> > > * *
> > > * Dr. Niharendu Choudhury Tel: 91-22-2559 5089 *
> > > * Theoretical Chemistry Section, Fax: 91-22-2550 5151 *
> > > * RC & CD Division, Chemistry Group, 91-22-2551-9613 *
> > > * Mod. Lab, Email: nihcho at barc.gov.in *
> > > * Trombay, Mumbai-400 085 *
> > > * INDIA *
> > > * *
> > > * Residence Tel. No. 91-22-2552 7832 *
> > > *************************************************************************
> > >
> > >
> > > -------------------------------------------------
> > >
> > > _______________________________________________
> > > gmx-users mailing list gmx-users at gromacs.org
> > > http://www.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-request at gromacs.org.
> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > >
> > >
> > > _______________________________________________
> > > gmx-users mailing list gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please search the archive at http://www.gromacs.org/search before posting!
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> > > www interface or send it to gmx-users-request at gromacs.org.
> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > >
> >
> >
> >
> > *************************************************************************
> > * *
> > * Dr. Niharendu Choudhury Tel: 91-22-2559 5089 *
> > * Theoretical Chemistry Section, Fax: 91-22-2550 5151 *
> > * RC & CD Division, Chemistry Group, 91-22-2551-9613 *
> > * Mod. Lab, Email: nihcho at barc.gov.in *
> > * Trombay, Mumbai-400 085 *
> > * INDIA *
> > * *
> > * Residence Tel. No. 91-22-2552 7832 *
> > *************************************************************************
> >
> >
> > -------------------------------------------------
> >
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
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>
>
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> End of gmx-users Digest, Vol 47, Issue 58
> *****************************************
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