<div class="gmail_quote">I have replaced all HW by H in ffnonbonded.itp.After executing the command:<br>grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr
<font size="3"><font face="Arial"><br></font></font><br>I am getting this error:<font size="3"><font face="Arial"><br></font></font><br>File input/output error:<font size="3"><font face="Arial"><br></font></font>dppc128.gro<font size="3"><font face="Arial"><br>
<br></font></font>should I replace all HW with H (without delecting numbers that is given in dppc128.pdb alongwith HW) in dppc128.pdb file?<br><font face="Arial"><font size="3"><pre><br><br></pre></font></font><br><br><br>
<br><br>On Mon, Jan 23, 2012 at 6:41 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">
<div>
<div><br><br>Anushree Tripathi wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">I am going through the Justin Lemku tutorial for KALP15 in DPPC. I have<br>reached step three, when I try to generate a trp file for DPPC only by<br>
means of :<br><br>grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr<br><br>I get the following warning:<br><br>Fatal error:<br>Atomtype OW not found<br><br>Any idea as to what causes this problem?<br></blockquote>
<br></div></div>You constructed the force field incorrectly by deleting or commenting out a line (or more) related to OW. Re-check the instructions provided in the tutorial.<br><br>-Justin<br><br>-- <br>==============================<u></u>==========<br>
<br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]<a href="http://vt.edu/" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br><br>==============================<u></u>==========<span><font color="#888888"><br>
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