<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span></span><span>Dear All,</span></div><div style="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;"><div id="yiv360996897"><div><div style="color: rgb(0, 0, 0); font-family: times new roman, new york, times, serif; font-size: 12pt; background-color: rgb(255, 255, 255);"><div><span></span> </div><div><span>The problem has been solved.</span></div><div><span></span> </div><div><span>When I cp the pdb file from another folder to the gromacs running folder, I find the pdb file in the gromacs running folder was not permitted to open, even by "vi"..</span></div><div><span></span> </div><div><span>Then in the normal Windows system I copy the pdb file in its original folder and paste it into the gromacs running
folder, in cygwin gromcas the pab can be read (or can be open by vi).</span></div><div><span></span> </div><div><span>But there is still ununderstandable why by cp the pdb file is not permitted to
open.</span></div><div><span></span> </div><div><span>Cheers,</span></div><div><span></span> </div><div><span>Acoot</span></div><div><br></div> <div style="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;"> <div dir="ltr"> <font size="2" face="Arial"> <div style="margin: 5px 0px; padding: 0px; border: 1px solid rgb(204, 204, 204); height: 0px; line-height: 0; font-size: 0px;" class="yiv360996897hr"></div> <b><span style="font-weight: bold;">From:</span></b> Tsjerk Wassenaar <tsjerkw@gmail.com><br> <b><span style="font-weight: bold;">To:</span></b> Acoot Brett <acootbrett@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Thursday, 22 March 2012 4:24 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re:
[gmx-users] pdb2gmx input file error<br> </font> </div> <br><div id="yiv360996897"><div>Hi Acoot,</div>
<div>What do you mean with 'not at all'? What is the output of pdb2gmx? Did you check what is in those pdb files?</div>
<div>Cheers,</div>
<div>Tsjerk</div>
<blockquote type="cite">On Mar 22, 2012 5:06 AM, "Acoot Brett" <<a href="mailto:acootbrett@yahoo.com" rel="nofollow" target="_blank" ymailto="mailto:acootbrett@yahoo.com">acootbrett@yahoo.com</a>> wrote:<br><br><div><div style="font-family: times new roman, new york, times, serif; font-size: 12pt;">
<div>Dear All,</div><div> </div><div>I find some pdb files downloaded from RCSB cannot be recognized by pdb2gmx at all.</div><div> </div><div>Is any server which can convert and RCSB pdb files to files readable by pdb2gmx?</div>
<div> </div><div>Cheers,</div><div> </div><div>Acoot</div></div></div><br>--<br>
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