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On 2/01/2012 12:35 AM, Saba Ferdous wrote:
<blockquote
cite="mid:CANTGNo4SjZauVV8rEHMT8YYgdeurB-i-AG6G3mbU6CghXV15ng@mail.gmail.com"
type="cite"><br clear="all">
<div><span
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">Dear
Gromacs Experts,</span></div>
<div><span
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)"><br>
</span></div>
<div><span
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">I
am having problem in execution of a command in Gromacs,</span><br
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<br
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<span
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">thats
when i use dssp for secondary structure analysis.</span><br
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<br
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<span
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">it
gives error:</span><br
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<br
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<span
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">Reading
file md_0_10.tpr, VERSION 4.5.5 (single precision)</span><br
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<span
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">Reading
file md_0_10.tpr, VERSION 4.5.5 (single precision)</span><br
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<span
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(204,204,204)">Segmentation
fault (core dumped)</span><br
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<span
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">saba@linuxserver:~/complex/MD></span><br
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<br
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)"
clear="all">
<span
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">I
used the command : ulimit -s unlimited</span><br
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<span
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)"> </span><span
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
ulimit -c unlimited</span><br
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<span
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">but
no vain, the problem still persists, </span><br
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<span
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">Tell
me how to fix it?????</span></div>
<br>
</blockquote>
<br>
Assuming other GROMACS tools work, you've done something wrong with
the DSSP installation, but it's impossible for us to say what. Note
that the version of DSSP released on the last year or two is
unsuitable - get the old one.<br>
<br>
Mark<br>
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