<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; ">Hi,</div><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "> I have a protein pdb file with ACE as N-cap and I am trying to use pdb2gmx ( within gromacs 4.5.4 ) to generate a topology file using opls/AA . the ACE is present in opls aminoacids.rtp files. But, on issuing the pdb2gmx command, I get following error message:</div><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "><br></div><div><div><font class="Apple-style-span" face="'times new roman', 'new york', times, serif">Program pdb2gmx_44, VERSION 4.5.4</font></div><div><font class="Apple-style-span" face="'times new roman', 'new york', times, serif">Source code file: pdb2top.c, line:
1070</font></div><div><font class="Apple-style-span" face="'times new roman', 'new york', times, serif"><br></font></div><div><font class="Apple-style-span" face="'times new roman', 'new york', times, serif">Fatal error:</font></div><div><font class="Apple-style-span" face="'times new roman', 'new york', times, serif">atom N not found in buiding block 1ACE while combining tdb and rtp</font></div><div><font class="Apple-style-span" face="'times new roman', 'new york', times, serif">For more information and tips for troubleshooting, please check the GROMACS</font></div><div><font class="Apple-style-span" face="'times new roman', 'new york', times, serif">website at http://www.gromacs.org/Documentation/Errors</font></div><div><font class="Apple-style-span" face="'times new roman', 'new york', times, serif"><br></font></div><div><font class="Apple-style-span" face="'times new roman', 'new york', times, serif">I wonder how I can make sure that ACE can be
used as N-terminus.</font></div><div><font class="Apple-style-span" face="'times new roman', 'new york', times, serif"><br></font></div><div><font class="Apple-style-span" face="'times new roman', 'new york', times, serif">Sanku</font></div></div></div></body></html>