Hello!<br>
<br>
Since you have modelled the structure, so the important thing is the
position of the heavy atoms and not of the hydrogens, you can just do
what GROMACS asks you to do:<br>
<br>
pdb2gmx ..... (all the things that you have to put) ...... -ignh<br>
<br>
This flag will make pdb2gmx ignore the hydrogens and replace them.<br>
<br>
Hope it helps!<br>
<br>
Cheers,<br>
Annalisa<br>
<br>
-----------------------------------------------------------------------<br>
Annalisa Bordogna - PhD. student<br>
Universita` degli Studi di Milano - Bicocca - Italy<br>
<br>
<br><br><div><span class="gmail_quote">2010/2/8, bharat gupta <<a href="mailto:bharat.85.monu@gmail.com" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">bharat.85.monu@gmail.com</a>>:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi all,<br> <br> I have modelled a structure and I want to minimize it using GROMACS<br> but while generating the topology file using pdb2gmx command I am<br> getting the following error :-<br> <br> Atom HN1 in residue LEU 1 not found in rtp entry with 9 atoms<br>
while sorting atoms. Maybe different protonation state.<br>
Remove this hydrogen or choose a different protonation state.<br> Option -ignh will ignore all hydrogens in the input.<br> <br> <br> <br> <br> Can anyone help me out to rectify this error<br> <br> --<br> Bharat<br>
M.Sc. Bioinformatics (Final year)<br> Centre for Bioinformatics<br> Pondicherry University<br> Puducherry<br> India<br> Mob. +919962670525<br> <br>--<br> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">http://www.gromacs.org/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" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">http://www.gromacs.org/mailing_lists/users.php</a><br>
</blockquote></div><br>