<DIV><SPAN>On 18/04/12, <B class=name>aiswarya pawar </B><aiswarya.pawar@gmail.com> wrote:</SPAN></DIV><BLOCKQUOTE style="BORDER-LEFT: #00f 1px solid; PADDING-LEFT: 13px; MARGIN-LEFT: 0px" class=iwcQuote cite=mid:CAEa6cRAhGQSE0yg_A4oV-3PO3BU=LvajZV9GTgeEthqz4buvrQ@mail.gmail.com type="cite">
<DIV class="mimepart text html">Hi Users,<br /><br />I did the following step=<br /> pdb2gmx -ignh -f 1ahw.pdb -o sample.pdb -p sample.top<BR clear=all><br /><br />and received an error= Atom ND1 not found in residue <a href="http://seq.nr/" target=1 >seq.nr</A>. 7 while adding atom.<br /><br />I dont understand how do i rectify this.</DIV></BLOCKQUOTE>
<DIV> </DIV><DIV>You're telling pdb2gmx to ignore hydrogens in the input, so it's trying to add them back, but the residue it identifies as number 7 doesn't have atom ND1 that is required to build some atom (probably a hydrogen). So your residue and/or atom naming is not what GROMACS requires for your force field.</DIV><DIV> </DIV><DIV>Mark</DIV>