<br /><br /><span>On 25/05/11, <b class="name">Jon Fuller </b> <jonathan.fuller@gmail.com> wrote:</span><blockquote cite="mid:BANLkTi=GFr5aOQ6UqpAXpkM8K5J7NHTmqQ@mail.gmail.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text plain">Dear all,<br /><br />I thought that I would reply to this thread as I am having similar<br />problems and there didn't seem to be an obvious solution.<br />I wanted to run a simulation of a POPE bilayer using the Charmm36<br />parameters from the Gromacs website. So I used pdb2gmx to generate a<br />.top file.<br /><br />I used the input file from this website:<br />wget <a href="http://terpconnect.umd.edu/~jbklauda/research/download/pope80-c36npt.pdb" target="l">http://terpconnect.umd.edu/~jbklauda/research/download/pope80-c36npt.pdb</a><br /><br />pdb2gmx -f pope80-c36npt.pdb -o pope.pdb -p pope.top -ff charmm36<br />(I then selected option 3 (tips3p charmm water))<br /><br />I found that whilst pdb2gmx completes 'successfully', no bond, angle<br />or dihedral terms are generated in the resulting top file.</div></blockquote><br />I don't understand what you think the problem is. The .top file from
which you included excerpts clearly has sections for such terms, and the
pdb2gmx output reports generating such.<br /><br />Mark