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Hi,<br><br>I assume this is 4.0 and not 4.0.2, right?<br>I fixed the problem of not having a box in editconf in 4.0.2.<br><br>Berk<br><br><hr id="stopSpelling">Date: Thu, 20 Nov 2008 16:22:44 +0000<br>From: alanwilter@gmail.com<br>To: gmx-users@gromacs.org<br>Subject: [gmx-users] problems with editconf 4.0<br><br>Hello,<div><br></div><div>So this command used to work fine:</div><div><br></div><div><pre class="EC_prettyprint" style="border-left: 3px solid rgb(204, 204, 204); padding: 0.5em; font-size: 110%; margin-left: 2em;"><span class="EC_pln" style="color: rgb(0, 0, 0);">editconf </span><span class="EC_pun" style="color: rgb(102, 102, 0);">-</span><span class="EC_pln" style="color: rgb(0, 0, 0);">bt triclinic </span><span class="EC_pun" style="color: rgb(102, 102, 0);">-</span><span class="EC_pln" style="color: rgb(0, 0, 0);">f </span><span class="EC_typ" style="color: rgb(102, 0, 102);">Complex</span><span class="EC_pun" style="color: rgb(102, 102, 0);">.</span><span class="EC_pln" style="color: rgb(0, 0, 0);">pdb </span><span class="EC_pun" style="color: rgb(102, 102, 0);">-</span><span class="EC_pln" style="color: rgb(0, 0, 0);">o </span><span class="EC_typ" style="color: rgb(102, 0, 102);">Complex</span><span class="EC_pun" style="color: rgb(102, 102, 0);">.</span><span class="EC_pln" style="color: rgb(0, 0, 0);">pdb </span><span class="EC_pun" style="color: rgb(102, 102, 0);">-</span><span class="EC_pln" style="color: rgb(0, 0, 0);">d </span><span class="EC_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="EC_prettyprint" style="border-left: 3px solid rgb(204, 204, 204); padding: 0.5em; font-size: 110%; margin-left: 2em;"><span class="EC_pln" style="color: rgb(0, 0, 0);">genbox </span><span class="EC_pun" style="color: rgb(102, 102, 0);">-</span><span class="EC_pln" style="color: rgb(0, 0, 0);">cp </span><span class="EC_typ" style="color: rgb(102, 0, 102);">Complex</span><span class="EC_pun" style="color: rgb(102, 102, 0);">.</span><span class="EC_pln" style="color: rgb(0, 0, 0);">pdb </span><span class="EC_pun" style="color: rgb(102, 102, 0);">-</span><span class="EC_pln" style="color: rgb(0, 0, 0);">cs ffamber_tip3p</span><span class="EC_pun" style="color: rgb(102, 102, 0);">.</span><span class="EC_pln" style="color: rgb(0, 0, 0);">gro </span><span class="EC_pun" style="color: rgb(102, 102, 0);">-</span><span class="EC_pln" style="color: rgb(0, 0, 0);">o Complex_b4ion</span><span class="EC_pun" style="color: rgb(102, 102, 0);">.</span><span class="EC_pln" style="color: rgb(0, 0, 0);">pdb </span><span class="EC_pun" style="color: rgb(102, 102, 0);">-</span><span class="EC_pln" style="color: rgb(0, 0, 0);">p </span><span class="EC_typ" style="color: rgb(102, 0, 102);">Complex</span><span class="EC_pun" style="color: rgb(102, 102, 0);">.</span><span class="EC_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/%7Eawd28">http://www.bio.cam.ac.uk/~awd28</a><<<br>
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