Hello,<div><br></div><div>So this command used to work fine:</div><div><br></div><div><pre class="prettyprint" style="font-size: 110%; margin-left: 2em; padding-top: 0.5em; padding-right: 0.5em; padding-bottom: 0.5em; padding-left: 0.5em; border-left-width: 3px; border-left-style: solid; border-left-color: rgb(204, 204, 204); ">
<span class="pln" style="color: rgb(0, 0, 0); ">editconf </span><span class="pun" style="color: rgb(102, 102, 0); ">-</span><span class="pln" style="color: rgb(0, 0, 0); ">bt triclinic </span><span class="pun" style="color: rgb(102, 102, 0); ">-</span><span class="pln" style="color: rgb(0, 0, 0); ">f </span><span class="typ" style="color: rgb(102, 0, 102); ">Complex</span><span class="pun" style="color: rgb(102, 102, 0); ">.</span><span class="pln" style="color: rgb(0, 0, 0); ">pdb </span><span class="pun" style="color: rgb(102, 102, 0); ">-</span><span class="pln" style="color: rgb(0, 0, 0); ">o </span><span class="typ" style="color: rgb(102, 0, 102); ">Complex</span><span class="pun" style="color: rgb(102, 102, 0); ">.</span><span class="pln" style="color: rgb(0, 0, 0); ">pdb </span><span class="pun" style="color: rgb(102, 102, 0); ">-</span><span class="pln" style="color: rgb(0, 0, 0); ">d </span><span class="lit" style="color: rgb(0, 102, 102); ">1.0</span></pre>
Now, with gmx 4.0 (from fink for Mac Intel Leopard), I got a warning:</div><div><br></div><div>WARNING: No boxtype specified - distance condition applied in each dimension.</div><div><br></div><div>(no box information is inserted in the pdb file as it used to do in gmx 3)</div>
<div><br></div><div>and then when I try:</div><div><br></div><div><pre class="prettyprint" style="font-size: 110%; margin-left: 2em; padding-top: 0.5em; padding-right: 0.5em; padding-bottom: 0.5em; padding-left: 0.5em; border-left-width: 3px; border-left-style: solid; border-left-color: rgb(204, 204, 204); ">
<span class="pln" style="color: rgb(0, 0, 0); ">genbox </span><span class="pun" style="color: rgb(102, 102, 0); ">-</span><span class="pln" style="color: rgb(0, 0, 0); ">cp </span><span class="typ" style="color: rgb(102, 0, 102); ">Complex</span><span class="pun" style="color: rgb(102, 102, 0); ">.</span><span class="pln" style="color: rgb(0, 0, 0); ">pdb </span><span class="pun" style="color: rgb(102, 102, 0); ">-</span><span class="pln" style="color: rgb(0, 0, 0); ">cs ffamber_tip3p</span><span class="pun" style="color: rgb(102, 102, 0); ">.</span><span class="pln" style="color: rgb(0, 0, 0); ">gro </span><span class="pun" style="color: rgb(102, 102, 0); ">-</span><span class="pln" style="color: rgb(0, 0, 0); ">o Complex_b4ion</span><span class="pun" style="color: rgb(102, 102, 0); ">.</span><span class="pln" style="color: rgb(0, 0, 0); ">pdb </span><span class="pun" style="color: rgb(102, 102, 0); ">-</span><span class="pln" style="color: rgb(0, 0, 0); ">p </span><span class="typ" style="color: rgb(102, 0, 102); ">Complex</span><span class="pun" style="color: rgb(102, 102, 0); ">.</span><span class="pln" style="color: rgb(0, 0, 0); ">top</span></pre>
<div>I get this error:</div><div><br></div><div><div>-------------------------------------------------------</div><div>Program genbox, VERSION 4.0</div><div>Source code file: gmx_genbox.c, line: 744</div><div><br></div><div>
Fatal error:</div><div>Undefined solute box.</div><div>Create one with editconf or give explicit -box command line option</div><div>-------------------------------------------------------</div><div><br></div><div>If I change '-o Complex.pdb' to '-o Complex.gro' and so on (i.e, if I use gro instead of pdb), all work fine.</div>
<div><br></div><div>So, pdb format is not ok anymore with gmx commands or there's a bug here?</div><div><br></div><div>Many thanks in advance,</div><div>Alan</div></div>-- <br>Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate<br>
Department of Biochemistry, University of Cambridge.<br>80 Tennis Court Road, Cambridge CB2 1GA, UK.<br>>><a href="http://www.bio.cam.ac.uk/~awd28">http://www.bio.cam.ac.uk/~awd28</a><<<br>
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