<DIV> </DIV><DIV> </DIV><SPAN>On 05/04/12, <B class=name>James Starlight </B><jmsstarlight@gmail.com> wrote:</SPAN>
<BLOCKQUOTE style="BORDER-LEFT: #00f 1px solid; PADDING-LEFT: 13px; MARGIN-LEFT: 0px" class=iwcQuote cite=mid:CAALQopyqdizVKKRf+wcOQ6JEPGw4zbHd9evgCqVBp0BvKVfziQ@mail.gmail.com type="cite">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 ?</BLOCKQUOTE>
<DIV> </DIV><DIV>Use trjconv -n and tpbconv -n to create a matching subset of your trajectory and -s input file, and use that as input to g_saltbr. </DIV><DIV> </DIV><BLOCKQUOTE style="BORDER-LEFT: #00f 1px solid; PADDING-LEFT: 13px; MARGIN-LEFT: 0px" class=iwcQuote cite=mid:CAALQopyqdizVKKRf+wcOQ6JEPGw4zbHd9evgCqVBp0BvKVfziQ@mail.gmail.com type="cite"><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?</TT></B></BLOCKQUOTE>
<DIV> </DIV><DIV>Looks like Rmax to me, from g_saltbr -h, but if you experiment, find out and report back it can go into the next version of the documentation (which is never perfect!).</DIV><DIV> </DIV><DIV>Mark </DIV><DIV> </DIV><BLOCKQUOTE style="BORDER-LEFT: #00f 1px solid; PADDING-LEFT: 13px; MARGIN-LEFT: 0px" class=iwcQuote cite=mid:CAALQopyqdizVKKRf+wcOQ6JEPGw4zbHd9evgCqVBp0BvKVfziQ@mail.gmail.com type="cite">
<DIV class="mimepart text html"><B><TT><br /><br />James<br /></TT></B><br />
<DIV class=gmail_quote>5 апреля 2012 г. 12:36 пользователь Peter C. Lai <SPAN dir=ltr><<a href="mailto:pcl@uab.edu" >pcl@uab.edu</A>></SPAN> написал:<br />
<BLOCKQUOTE style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class=gmail_quote>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=1 >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=1 >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=1 >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=1 >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>
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<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=1 >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=1 >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=1 >http://www.gromacs.org/Support/Mailing_Lists</A><br /></DIV></DIV></BLOCKQUOTE></DIV><br /></DIV></BLOCKQUOTE>
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