Hi Anirban,<br><br>I have also followed Justin sir's tutorial.<br>You should not remove the OW entries.<br>You can remove the HW entries for sure and then this will work.<br><br>Regards,<br>Pawan<br><br><div class="gmail_quote">
On Tue, May 12, 2009 at 9:45 AM, Anirban Ghosh <span dir="ltr"><<a href="mailto:anirbanz83@yahoo.co.in">anirbanz83@yahoo.co.in</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td style="font-family: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; font-size: inherit; line-height: inherit; font-size-adjust: inherit; font-stretch: inherit;" valign="top">
Hello Justin,<br><br>Thanks a lot for the reply. Your tutorial is indeed very good.<br>I followed your
tutorial on protein-lipid simulation. I added the non-bonded parameters
from the lipid.itp file to the ffG53a6nb_lipid.itp file. You have told
to either delete the atom-type HW entries having zero values in the
non-bonded section or replace them with H. But the HW values are not
zero. And they are also present in the "pairlist" section. So should I
change in this section also? And when I am running the grompp command I
am getting the error "Atom-type OW not found". So should I also delete
the OW entries or should I replace them? If replace, then with what?
Should I replace all the OW and HW entries throughout the
ffG53a6nb_lipid.itp file? Please advice.<div class="im"><br><br>Regards,<br><br><div><font color="#0000bf" size="4"></font> </div><div style="color: rgb(0, 0, 191);"><b>Anirban Ghosh</b></div><div style="color: rgb(0, 0, 191);">
<b>Grade Based Engineer<br>Bioinformatics Team<br>Centre for Development of Advanced Computing (C-DAC)<br>Pune, India<br></b></div></div></td></tr></tbody></table><br>
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