<html>
<head>
<style>
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
FONT-SIZE: 10pt;
FONT-FAMILY:Tahoma
}
</style>
</head>
<body class='hmmessage'><div style="text-align: left;"><br></div><br><br><br><hr id="stopSpelling">> From: gmx-users-request@gromacs.org<br>> Subject: gmx-users Digest, Vol 47, Issue 58<br>> To: gmx-users@gromacs.org<br>> Date: Tue, 18 Mar 2008 12:00:06 +0100<br>> <br>> Send gmx-users mailing list submissions to<br>> gmx-users@gromacs.org<br>> <br>> To subscribe or unsubscribe via the World Wide Web, visit<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> or, via email, send a message with subject or body 'help' to<br>> gmx-users-request@gromacs.org<br>> <br>> You can reach the person managing the list at<br>> gmx-users-owner@gromacs.org<br>> <br>> When replying, please edit your Subject line so it is more specific<br>> than "Re: Contents of gmx-users digest..."<br>> <br>> <br>> Today's Topics:<br>> <br>> 1. RE: average structure with ligand (#NGUYEN CONG TRI#)<br>> 2. Re: average structure with ligand (Ran Friedman)<br>> 3. RE: Force field (?ngel Pi?eiro)<br>> <br>> <br>> ----------------------------------------------------------------------<br>> <br>> Message: 1<br>> Date: Tue, 18 Mar 2008 17:15:42 +0800<br>> From: "#NGUYEN CONG TRI#" <NGUY0045@ntu.edu.sg><br>> Subject: RE: [gmx-users] average structure with ligand<br>> To: "Discussion list for GROMACS users" <gmx-users@gromacs.org><br>> Message-ID:<br>> <E476542CD98D094999A0FF7E022A465C013B1A57@MAIL23.student.main.ntu.edu.sg><br>> <br>> Content-Type: text/plain; charset="iso-8859-1"<br>> <br>> Dear Anna,<br>> <br>> I think you can use make_ndx to make a new group for your ligand+protein. For example: <br>> $make_ndx -f filename.gro -o filename.ndx<br>> 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. <br>> Hope this can help.<br>> <br>> Regards,<br>> Tri.<br>> <br>> ________________________________<br>> <br>> From: gmx-users-bounces@gromacs.org on behalf of Anna Marabotti<br>> Sent: Tue 3/18/2008 4:47 PM<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] average structure with ligand<br>> <br>> <br>> <br>> Dear gmx-users,<br>> I would like to create from my trajectory an average structure of my protein with its ligand inside.<br>> With both g_rmsf and g_cluster I am prompted to indicate one group, but ligand and protein are<br>> separated into different groups, and I'd want to exclude water from this structure, so I don't want<br>> to indicate "system". I checked into the mailing list but didn't find any suggestion. Does anybody<br>> has one?<br>> Many thanks in advance and regards<br>> Anna Marabotti<br>> <br>> ______________________________________________<br>> Anna Marabotti, Ph.D.<br>> Laboratorio di Bioinformatica e Biologia Computazionale<br>> Istituto di Scienze dell'Alimentazione, CNR<br>> Via Roma 52 A/C<br>> 83100 Avellino (Italy)<br>> Tel: +39 0825 299651<br>> Fax: +39 0825 781585<br>> Skype: annam1972<br>> E-mail: amarabotti@isa.cnr.it<br>> Web page: http://bioinformatica.isa.cnr.it/anna.htm<br>> ____________________________________________________<br>> "If you think you are too small to make a difference, try sleeping with a mosquito"<br>> <br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the<br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> <br>> <br>> -------------- next part --------------<br>> A non-text attachment was scrubbed...<br>> Name: not available<br>> Type: application/ms-tnef<br>> Size: 4998 bytes<br>> Desc: not available<br>> Url : http://www.gromacs.org/pipermail/gmx-users/attachments/20080318/9f185c6b/attachment-0001.bin<br>> <br>> ------------------------------<br>> <br>> Message: 2<br>> Date: Tue, 18 Mar 2008 10:16:01 +0100<br>> From: Ran Friedman <r.friedman@bioc.uzh.ch><br>> Subject: Re: [gmx-users] average structure with ligand<br>> To: Discussion list for GROMACS users <gmx-users@gromacs.org><br>> Message-ID: <47DF8851.4030805@bioc.uzh.ch><br>> Content-Type: text/plain; charset=ISO-8859-1<br>> <br>> Dear Anna,<br>> <br>> Use make_ndx to create any group you find useful.<br>> <br>> Ran.<br>> <br>> Anna Marabotti wrote:<br>> > Dear gmx-users,<br>> > I would like to create from my trajectory an average structure of my protein with its ligand inside.<br>> > With both g_rmsf and g_cluster I am prompted to indicate one group, but ligand and protein are<br>> > separated into different groups, and I'd want to exclude water from this structure, so I don't want<br>> > to indicate "system". I checked into the mailing list but didn't find any suggestion. Does anybody<br>> > has one?<br>> > Many thanks in advance and regards<br>> > Anna Marabotti<br>> ><br>> > ______________________________________________<br>> > Anna Marabotti, Ph.D.<br>> > Laboratorio di Bioinformatica e Biologia Computazionale<br>> > Istituto di Scienze dell'Alimentazione, CNR<br>> > Via Roma 52 A/C<br>> > 83100 Avellino (Italy)<br>> > Tel: +39 0825 299651<br>> > Fax: +39 0825 781585<br>> > Skype: annam1972<br>> > E-mail: amarabotti@isa.cnr.it<br>> > Web page: http://bioinformatica.isa.cnr.it/anna.htm<br>> > ____________________________________________________<br>> > "If you think you are too small to make a difference, try sleeping with a mosquito"<br>> ><br>> > _______________________________________________<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at http://www.gromacs.org/search before posting!<br>> > Please don't post (un)subscribe requests to the list. Use the <br>> > www interface or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> ><br>> > <br>> <br>> <br>> -- <br>> ------------------------------------------------------<br>> Ran Friedman<br>> Postdoctoral Fellow<br>> Computational Structural Biology Group (A. Caflisch)<br>> Department of Biochemistry<br>> University of Zurich<br>> Winterthurerstrasse 190<br>> CH-8057 Zurich, Switzerland<br>> Tel. +41-44-6355593<br>> Email: r.friedman@bioc.unizh.ch<br>> Skype: ran.friedman<br>> ------------------------------------------------------<br>> <br>> <br>> <br>> ------------------------------<br>> <br>> Message: 3<br>> Date: Tue, 18 Mar 2008 10:38:29 +0100<br>> From: ?ngel Pi?eiro <fangel@usc.es><br>> Subject: RE: [gmx-users] Force field<br>> To: Discussion list for GROMACS users <gmx-users@gromacs.org><br>> Message-ID: <1205833109.31216.65.camel@lysine><br>> Content-Type: text/plain; charset=utf-8<br>> <br>> Hi Nihar,<br>> unfortunately I can't help you with thioflavin parameterization and<br>> probably other people here will address you to general links. Our CDs<br>> were built on the base of topologies for smaller sugars already<br>> available in the gromos force field (pasting building blocks). I hope<br>> someone else can help you with thioflavin...<br>> <br>> Regards,<br>> <br>> Angel.<br>> <br>> <br>> On Tue, 2008-03-18 at 10:11 +0530, Dr. Niharendu Choudhury wrote:<br>> > Hi �ngel,<br>> > Thanks a lot for coming forward. Regarding CD (\alpha, \beta and \gamma) I <br>> > will contact you as soon as possible. For the moment I would like to get <br>> > the same for Thioflavin-T. It is a fairly big molecules with I think 39 <br>> > atoms. Can you tell me how go about (procedure in detail) to get the FF <br>> > from QM calculation?<br>> > <br>> > I must thank you again.<br>> > <br>> > Nihar<br>> > <br>> > Quoting �ngel Piñeiro <fangel@usc.es>:<br>> > <br>> > > Dear Nihar,<br>> > > if you contact me off the list I could send to you itp files for native<br>> > > alpha, beta, and gamma cyclodextrins compatible with the gromos forcefield<br>> > > (the ones we used in "jpcb (2007) 4383" and "jpcb (2007) 12625").<br>> > > Unfortunately I do not have the thioflavin.<br>> > > <br>> > > Regards,<br>> > > <br>> > > Angel Piñeiro.<br>> > > <br>> > > <br>> > > -----Mensaje original-----<br>> > > De: gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org] En<br>> > > nombre de Dr. Niharendu Choudhury<br>> > > Enviado el: sábado, 15 de marzo de 2008 02:54 a.m.<br>> > > Para: Discussion list for GROMACS users<br>> > > Asunto: [gmx-users] Force field<br>> > > <br>> > > Hi GROMACS users,<br>> > > I would like to study cyclodextrin + Thioflavin T in water. Is there any<br>> > > forcefiled parameters for these in any of the force-field supplied with <br>> > > GROMACS? <br>> > > <br>> > > It will be extremely beneficial if anybody can supply field compatible with <br>> > > GROMACS OR force-field parameters for CHARMM like potential functions.<br>> > > <br>> > > Sincerely<br>> > > Nihar<br>> > > <br>> > > *************************************************************************<br>> > > * *<br>> > > * Dr. Niharendu Choudhury Tel: 91-22-2559 5089 *<br>> > > * Theoretical Chemistry Section, Fax: 91-22-2550 5151 *<br>> > > * RC & CD Division, Chemistry Group, 91-22-2551-9613 *<br>> > > * Mod. Lab, Email: nihcho@barc.gov.in *<br>> > > * Trombay, Mumbai-400 085 *<br>> > > * INDIA *<br>> > > * *<br>> > > * Residence Tel. No. 91-22-2552 7832 *<br>> > > *************************************************************************<br>> > > <br>> > > <br>> > > -------------------------------------------------<br>> > > <br>> > > _______________________________________________<br>> > > gmx-users mailing list gmx-users@gromacs.org<br>> > > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > > Please search the archive at http://www.gromacs.org/search before posting!<br>> > > Please don't post (un)subscribe requests to the list. Use the <br>> > > www interface or send it to gmx-users-request@gromacs.org.<br>> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> > > <br>> > > <br>> > > _______________________________________________<br>> > > gmx-users mailing list gmx-users@gromacs.org<br>> > > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > > Please search the archive at http://www.gromacs.org/search before posting!<br>> > > Please don't post (un)subscribe requests to the list. Use the <br>> > > www interface or send it to gmx-users-request@gromacs.org.<br>> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> > > <br>> > <br>> > <br>> > <br>> > *************************************************************************<br>> > * *<br>> > * Dr. Niharendu Choudhury Tel: 91-22-2559 5089 *<br>> > * Theoretical Chemistry Section, Fax: 91-22-2550 5151 *<br>> > * RC & CD Division, Chemistry Group, 91-22-2551-9613 *<br>> > * Mod. Lab, Email: nihcho@barc.gov.in *<br>> > * Trombay, Mumbai-400 085 *<br>> > * INDIA *<br>> > * *<br>> > * Residence Tel. No. 91-22-2552 7832 *<br>> > *************************************************************************<br>> > <br>> > <br>> > -------------------------------------------------<br>> > <br>> > _______________________________________________<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at http://www.gromacs.org/search before posting!<br>> > Please don't post (un)subscribe requests to the list. Use the <br>> > www interface or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> <br>> <br>> <br>> ------------------------------<br>> <br>> _______________________________________________<br>> gmx-users mailing list<br>> gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> <br>> End of gmx-users Digest, Vol 47, Issue 58<br>> *****************************************<br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
</html>