Hi Leila,<br><br>I would try the other suggested options like catdcd or vmd. The script is a pain and you would have to adapt it to work with DNA. It cost me a lot of time.<br><br>I used g_hbond for residence time like this:<br>
<br>g_hbond -f 8_fullMD_CA.xtc -s 7_fullMD.tpr -n g_hbond.ndx -a 170 -num > g_hbond.log <font size="4">//the tpr file can't have restraints in it for some reason, thats why it is 7 and not 8. <br>// ndx file has the 3 atoms in the hbond</font> <br>
<br>Checking for overlap in atoms between 0SA and SER<br>Calculating hydrogen bonds between 0SA (1 atoms) and SER (2 atoms)<br>Found 1 donors and 2 acceptors<br><br>Will do grid-seach on 16x16x16 grid, rcut=0.35<br>Average number of hbonds per timeframe 0.872 out of 1 possible // <font size="4">so here's the % residence<br>
<br><font size="2">I found which residues were involved in hbonding to my ligand with an initial g_hbond run. I think you can get all the info you need from g_hbond.</font><br><br><font size="2">Oliver</font> </font><br>
<br><br><div class="gmail_quote">On 7 December 2010 11:37, leila karami <span dir="ltr"><<a href="mailto:karami.leila1@gmail.com">karami.leila1@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Dear Oliver<br><br>very thanks for your help.<br><br>Justin's perl script is good for direct hydrogen bonds, while I want to study water<br>mediated hydrogen bonds and residence time and occupation of them.<br><br>Are youe sure g_hbond give you residence time of hydrogen bonds?<br>
<br>before you said you used a script to change the pdb file for compatibility with amber.<br><br>please share me that.<br clear="all"><font color="#888888"><br>-- <br><pre style="font-family: arial,helvetica,sans-serif;">
Leila Karami<br>Ph.D. student of Physical Chemistry<br>
K.N. Toosi University of Technology<br>Theoretical Physical Chemistry Group</pre><br>
</font><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></blockquote></div><br>