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David wrote:<br>
<blockquote type="cite" cite="mid:1026284522.1396.0.camel@h241n2fls33o850.telia.com">
<pre wrap="">On Tue, 2002-07-09 at 21:53, <a class="moz-txt-link-abbreviated" href="mailto:storme@rpi.edu">storme@rpi.edu</a> wrote:<br></pre>
<blockquote type="cite">
<pre wrap="">Hi,<br> I am trying to build an eight alanine residue peptide capped at<br>either end with ACE and NAC. However, when I use pdb2gmx it gives me the<br>following error:<br><br>Fatal error: atom N not found in residue 1ACE while combining tdb and rtp<br><br>The error doesn't make a whole lot of sense since there is atom N in ACE.<br>If you have any ideas any help would be great. Thanks alot<br> <br></pre>
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<pre wrap=""><!---->There is ACE (CH3-CO) and NAC (NH2-CH3-CO) (I think). Check ffgmx.rtp<br> </pre>
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Hi,<br>
<br>
<br>
You will probably need to:<br>
<br>
1. Have at least the heavy atoms of the capping residue in your PDB file<br>
2. Use the '-ter' option to pdb2gmx and select 'no terminus' since you already
have capping residues.<br>
<br>
Cheers,<br>
<br>
Erik<br>
<br>
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