<div>Hi Tsjerk,</div> <div>Thanks for your help.You're right about "taking paths well walked by others,before starting new trails" but I have to do this simulation for my study:(<BR>Thanks very much for your suggestions again.</div> <div>Sincerely</div> <div>Fulya<BR><B><I>Tsjerk Wassenaar <tsjerkw@gmail.com></I></B> wrote:</div> <BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">Hi Fulya,<BR><BR>In addition to Mark's comments, if you have a friend who has the<BR>proper background for such parameterization he/she will know what to<BR>do and I don't need to describe the process. The basic thing is that<BR>if you're a novice with MD, it's best to first take the paths well<BR>walked by others, before starting new trails (in terms of<BR>methodology/parameters; I don't want to suggest to repeat projects<BR>from others, that's basically what tutorials are for, but I would<BR>advice to use proteins/dna with no
strings attached).<BR><BR>Regarding the mail server, the first two mails only arrived as<BR>forwarded mails, with a lot of junk around the main question (which<BR>makes reading less convenient).<BR><BR>Best,<BR><BR>Tsjerk<BR><BR>On 3/28/07, Mark Abraham <MARK.ABRAHAM@ANU.EDU.AU>wrote:<BR>> fulya caglar wrote:<BR>> > Hi Tsjerk,<BR>> > Do you know how can I add parameters for sulfite bound?You are right<BR>> > I have little experience in this field but maybe one of my friends can<BR>> > do this.I would be very grateful if you can explain parameterization<BR>> > briefly.<BR>><BR>> It's an involved process, which varies considerably depending on the<BR>> force field you're trying to extend. You should start by reading the<BR>> paper that describes the parameterization of the force field you're<BR>> trying to extend, and then thinking hard about how you can follow a<BR>> similar process to get parameters that are
consistent.<BR>><BR>> Mark<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>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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