<div> Hi Tsjerk,</div> <div> Do you know how can I add parameters for sulfite bound?You are right I have little experience in this field but maybe one of my friends can do this.I would be very grateful if you can explain parameterization briefly.</div> <div> </div> <div>And I dont think there is a problem with the mail server?Why did you ask?<BR><BR>Thank you very much!!!</div> <div>Sincerly</div> <div>Fulya<BR></div> <BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid"> <div> <HR SIZE=1> From: "Tsjerk Wassenaar" <tsjerkw@gmail.com><BR>To: "Discussion list for GROMACS users" <gmx-users@gromacs.org><BR>Subject: Re: [gmx-users] Fwd: How can I do the simulation of a protein with<BR>Tyr (SO3H)<BR><BR>Hi Fulya,<BR><BR>You can't just simulate everything you set your mind on. There are no<BR>parameters for sulfite bound tyrosine in the database (just what
it<BR>says). You have to add them yourself, which I don't recommend at this<BR>point, since it is clear you have but little experience in this field<BR>(and parameterization is an advanced topic).<BR><BR>By the way, do you have some problems with the mail server?<BR><BR>Best,<BR><BR>Tsjerk<BR><BR>On 3/27/07, fulya caglar <FULYACAGLAR@YAHOO.COM>wrote:<BR>><BR>><BR>> Note: forwarded message attached.<BR>><BR>> ________________________________<BR>> Bored stiff? Loosen up...<BR>> Download and play hundreds of games for free on Yahoo! Games.<BR>><BR>> ---------- Forwarded message ----------<BR>> From: fulya caglar <FULYACAGLAR@YAHOO.COM><BR>> To: Gromacs <GMX-USERS-REQUEST@GROMACS.ORG><BR>> Date: Tue, 27 Mar 2007 04:45:43 -0700 (PDT)<BR>> Subject: How can I do the simulation of a protein with Tyr (SO3H)<BR>><BR>> Hi!<BR>> I'm trying to do a simulation of a protein with bound sulfite ion (Tyr<BR>> (SO3H)).After the first command
( pdb2gmx) I am getting the following error<BR>> message :<BR>> -------------------------------------------------------------------------------------------------------------------------------------<BR>> Fatal error:<BR>> Residue 'SUL' not found in residue topology database<BR>> -------------------------------------------------------------------------------------------------------------------------------------<BR>><BR>> I would be very glad to know why I get this type of error and what can I do<BR>> about this. With thanks<BR>> Sincerely Fulya<BR>><BR>><BR>> ________________________________<BR>> TV dinner still cooling?<BR>> Check out "Tonight's Picks" on Yahoo! TV.<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<BR>> http://www.gromacs.org/mailing_lists/users.php<BR>><BR><BR><BR>-- <BR>Tsjerk A. Wassenaar, Ph.D.<BR>Junior UD (post-doc)<BR>Biomolecular NMR, Bijvoet Center<BR>Utrecht University<BR>Padualaan 8<BR>3584 CH Utrecht<BR>The Netherlands<BR>P: +31-30-2539931<BR>F: +31-30-2537623<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></BLOCKQUOTE><BR><p> 
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