Bharat, Peter thanks for advises<br><br>I've checked g_saltbr but not found possible definition of the specified regions ( this utility lacks -n index.ndx option). How I could ignore contacts between solvent and protein ?<br>
<br>Also what is the real <b><tt>-t value should I provide ? As I understood this is only Rmin but could I define Rmax cutoff as well?<br><br>James<br></tt></b><br><div class="gmail_quote">5 มะาลฬั 2012ว. 12:36 ะฯฬฺุฯืมิลฬุ Peter C. Lai <span dir="ltr"><<a href="mailto:pcl@uab.edu">pcl@uab.edu</a>></span> ฮมะษำมฬ:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">g_saltbr?<br>
<br>
If you have salt bridges you already know about and want to look at, you<br>
can always go with g_dist per pair manually.<br>
<div class="im"><br>
On 2012-04-05 12:23:02PM +0400, James Starlight wrote:<br>
> Dear Gromacs Users!<br>
><br>
><br>
> I'd like to monitor origin and destabilisation of salt-bridges during<br>
> simulation time. In particular I want to define some charged residues<br>
> within selection groups to monitor both of intra-protein as well as<br>
> protein-protein interactions. In past I've used only<br>
</div>> g_hbond<<a href="http://manual.gromacs.org/online/g_hbond.html" target="_blank">http://manual.gromacs.org/online/g_hbond.html</a>>utillity to<br>
<div class="im">> monitor Hbonds within selection. Is there any specified program<br>
> for such task but with salt-bridges only ?<br>
><br>
><br>
> Thanks for help,<br>
><br>
> James<br>
<br>
</div><div class="im">> --<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
> Please don't post (un)subscribe requests to the list. Use the<br>
> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
<br>
<br>
--<br>
</div>==================================================================<br>
<span class="HOEnZb"><font color="#888888">Peter C. Lai | University of Alabama-Birmingham<br>
Programmer/Analyst | KAUL 752A<br>
Genetics, Div. of Research | 705 South 20th Street<br>
<a href="mailto:pcl@uab.edu">pcl@uab.edu</a> | Birmingham AL 35294-4461<br>
(205) 690-0808 |<br>
==================================================================<br>
</font></span><div class="HOEnZb"><div class="h5"><br>
--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</div></div></blockquote></div><br>