@ram...<br>why dont u post what u did along with the part of the structure/file attached ...<br>and what is the error and what u did to rectify...<br><br>and as per as i know, if u are working with DNA system along with CHARMM forcefield, u should be careful with the atom types ...<br>
since u haven't mentioned. i think the O2 part is from DNA and adding that atom type in aminoacid file (aminoacid.rtp) may not serve ur purpose ............<br>please check which part does it belong to ( i think its the temini of DNA) and provide the proper aliases and use it ..<br>
<br>Thank u<br>Gurunath<br><br><br><div class="gmail_quote">On Sat, Jun 9, 2012 at 6:43 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</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"><div class="im">On 9/06/2012 11:08 PM, ramaraju801 wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
as i said my system is an protein-DNA complex and the error popped up only<br>
for atoms in DNA residues.<br>
</blockquote>
<br></div>
That's about 1% of the detail you'll need to provide in order for it to be worth any more of anybody's time helping you :-) See <a href="http://www.gromacs.org/Support" target="_blank">http://www.gromacs.org/Support</a> for advice on how to effectively ask for help. A complete description of your system contents, and copied and pasted input and output is essential. You already know from past threads that your termini are an issue, so make sure you focus on those details.<span class="HOEnZb"><font color="#888888"><br>
<br>
Mark</font></span><div class="HOEnZb"><div class="h5"><br>
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