<div class="gmail_quote">2009/10/6 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span></div><div class="gmail_quote"><br></div><div class="gmail_quote"><span dir="ltr"></span>Hi again! Thank you very much for the swift reply!<br>
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If you want to use pdb2gmx, you will need to create all the standard files (.rtp, .hdb, nb.itp, bon.itp, etc), create an entry in FF.dat, and increment the counter at the top of FF.dat.<br></blockquote><div><br></div><div>
Ah, I'm actually already in the process of writing a script to do that convert my force field files. :) Regarding this though (which I just realised that I should also have asked earlier) - since I am not actually doing any protein simulations or anything that has amino acids in it, do I still need the the <i>.rtp</i>, <i>.hdb</i>, <i>.ddb</i> files for <i>pdb2mgx</i> to work correctly?</div>
<div><br></div><div>I did try to increment the counter at the top of <i>FF.dat</i> before I sent the last e-mail but it didn't seem to work (or is that because I was missing files?).</div><div><br></div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Otherwise, it is relatively simple to write your own topology for a limited number of species as .itp files. See Chapter 5 of the manual for the format and requirements of all of these files.<br></blockquote><div><br></div>
<div>I have considered that option and read the manual already. :) It seems to be easier (for someone else who will be picking up where I will have left off) that I get the script running and have <i>pdb2gmx</i> do the job.</div>
<div><br></div><div>Once again, thank you very much and, again, thank you very much in advance!</div><div><br></div><div>Kind regards</div><div><br></div><div><br></div><div>Honman</div></div>