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On 11/05/2012 6:43 PM, Marzinek, Jan wrote:
<blockquote
cite="mid:787E9EFEEFC7384580812E4CA26D4F4409FE769D@icexch-m4.ic.ac.uk"
type="cite">
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Dear Gmx Users,<br>
<br>
Many of you probably faced an error:<br>
<br>
"An input file contains a line longer than 4095 characters,
while the buffer passed to fgets2 has size 4095. The line starts
with: '20s' "<br>
<br>
As I noted this error comes from the changes in the topology.
Gromacs somehow add " _ " and thus this problem occurs. For
instance:<br>
<br>
<br>
<p class="MsoNormal" style="tab-stops:36.75pt 73.5pt 110.25pt
147.0pt 183.75pt 220.5pt 257.25pt 294.0pt 330.75pt 367.5pt
404.25pt 441.0pt 477.75pt 514.5pt 551.25pt 588.0pt 624.75pt
661.5pt 698.25pt 735.0pt 771.75pt 808.5pt 845.25pt 882.0pt
918.75pt 955.5pt 35.0cm 1029.0pt 1065.75pt 1102.5pt 1139.25pt
1176.0pt;
mso-layout-grid-align:none;text-autospace:none">
<span style="font-size:9.0pt;
font-family:"Courier
New";mso-ansi-language:EN-US;mso-fareast-language:EN-US">[
bonds ]</span></p>
<p class="MsoNormal" style="tab-stops:36.75pt 73.5pt 110.25pt
147.0pt 183.75pt 220.5pt 257.25pt 294.0pt 330.75pt 367.5pt
404.25pt 441.0pt 477.75pt 514.5pt 551.25pt 588.0pt 624.75pt
661.5pt 698.25pt 735.0pt 771.75pt 808.5pt 845.25pt 882.0pt
918.75pt 955.5pt 35.0cm 1029.0pt 1065.75pt 1102.5pt 1139.25pt
1176.0pt;
mso-layout-grid-align:none;text-autospace:none">
<span style="font-size:9.0pt;
font-family:"Courier
New";mso-ansi-language:EN-US;mso-fareast-language:EN-US">;<span
style="mso-spacerun:yes">
</span>ai<span style="mso-spacerun:yes"> </span>aj funct<span
style="mso-spacerun:yes">
</span>c0<span style="mso-spacerun:yes"> </span>c1<span
style="mso-spacerun:yes">
</span>c2<span style="mso-spacerun:yes"> </span>c3</span></p>
<p class="MsoNormal" style="tab-stops:36.75pt 73.5pt 110.25pt
147.0pt 183.75pt 220.5pt 257.25pt 294.0pt 330.75pt 367.5pt
404.25pt 441.0pt 477.75pt 514.5pt 551.25pt 588.0pt 624.75pt
661.5pt 698.25pt 735.0pt 771.75pt 808.5pt 845.25pt 882.0pt
918.75pt 955.5pt 35.0cm 1029.0pt 1065.75pt 1102.5pt 1139.25pt
1176.0pt;
mso-layout-grid-align:none;text-autospace:none">
<span style="font-size:9.0pt;
font-family:"Courier
New";mso-ansi-language:EN-US;mso-fareast-language:EN-US"><span
style="mso-spacerun:yes">
</span>1<span style="mso-spacerun:yes"> </span>2<span
style="mso-spacerun:yes">
</span>1 </span></p>
<p class="MsoNormal" style="tab-stops:36.75pt 73.5pt 110.25pt
147.0pt 183.75pt 220.5pt 257.25pt 294.0pt 330.75pt 367.5pt
404.25pt 441.0pt 477.75pt 514.5pt 551.25pt 588.0pt 624.75pt
661.5pt 698.25pt 735.0pt 771.75pt 808.5pt 845.25pt 882.0pt
918.75pt 955.5pt 35.0cm 1029.0pt 1065.75pt 1102.5pt 1139.25pt
1176.0pt;
mso-layout-grid-align:none;text-autospace:none">
<span style="font-size:9.0pt;
font-family:"Courier
New";mso-ansi-language:EN-US;mso-fareast-language:EN-US"><span
style="mso-spacerun:yes">
</span>1<span style="mso-spacerun:yes"> </span>3<span
style="mso-spacerun:yes">
</span>1 </span></p>
<p class="MsoNormal" style="tab-stops:36.75pt 73.5pt 110.25pt
147.0pt 183.75pt 220.5pt 257.25pt 294.0pt 330.75pt 367.5pt
404.25pt 441.0pt 477.75pt 514.5pt 551.25pt 588.0pt 624.75pt
661.5pt 698.25pt 735.0pt 771.75pt 808.5pt 845.25pt 882.0pt
918.75pt 955.5pt 35.0cm 1029.0pt 1065.75pt 1102.5pt 1139.25pt
1176.0pt;
mso-layout-grid-align:none;text-autospace:none">
<span style="font-size:9.0pt;
font-family:"Courier
New";mso-ansi-language:EN-US;mso-fareast-language:EN-US"><span
style="mso-spacerun:yes">
</span>1<span style="mso-spacerun:yes"> </span>4<span
style="mso-spacerun:yes">
</span>1 </span></p>
<p class="MsoNormal" style="tab-stops:36.75pt 73.5pt 110.25pt
147.0pt 183.75pt 220.5pt 257.25pt 294.0pt 330.75pt 367.5pt
404.25pt 441.0pt 477.75pt 514.5pt 551.25pt 588.0pt 624.75pt
661.5pt 698.25pt 735.0pt 771.75pt 808.5pt 845.25pt 882.0pt
918.75pt 955.5pt 35.0cm 1029.0pt 1065.75pt 1102.5pt 1139.25pt
1176.0pt;
mso-layout-grid-align:none;text-autospace:none">
<span style="font-size:9.0pt;
font-family:"Courier
New";mso-ansi-language:EN-US;mso-fareast-language:EN-US"><span
style="mso-spacerun:yes">
</span>4<span style="mso-spacerun:yes"> </span>5<span
style="mso-spacerun:yes">
</span>1 </span></p>
<p class="MsoNormal" style="tab-stops:36.75pt 73.5pt 110.25pt
147.0pt 183.75pt 220.5pt 257.25pt 294.0pt 330.75pt 367.5pt
404.25pt 441.0pt 477.75pt 514.5pt 551.25pt 588.0pt 624.75pt
661.5pt 698.25pt 735.0pt 771.75pt 808.5pt 845.25pt 882.0pt
918.75pt 955.5pt 35.0cm 1029.0pt 1065.75pt 1102.5pt 1139.25pt
1176.0pt;
mso-layout-grid-align:none;text-autospace:none">
<span style="font-size:9.0pt;
font-family:"Courier
New";mso-ansi-language:EN-US;mso-fareast-language:EN-US"><span
style="mso-spacerun:yes">
</span>4<span style="mso-spacerun:yes"> </span>6<span
style="mso-spacerun:yes">
</span>1 _</span></p>
<p class="MsoNormal" style="tab-stops:36.75pt 73.5pt 110.25pt
147.0pt 183.75pt 220.5pt 257.25pt 294.0pt 330.75pt 367.5pt
404.25pt 441.0pt 477.75pt 514.5pt 551.25pt 588.0pt 624.75pt
661.5pt 698.25pt 735.0pt 771.75pt 808.5pt 845.25pt 882.0pt
918.75pt 955.5pt 35.0cm 1029.0pt 1065.75pt 1102.5pt 1139.25pt
1176.0pt;
mso-layout-grid-align:none;text-autospace:none">
<span style="font-size:9.0pt;
font-family:"Courier
New";mso-ansi-language:EN-US;mso-fareast-language:EN-US"><span
style="mso-spacerun:yes">
</span>4<span style="mso-spacerun:yes"> </span>24<span
style="mso-spacerun:yes">
</span>1 </span></p>
<p class="MsoNormal" style="tab-stops:36.75pt 73.5pt 110.25pt
147.0pt 183.75pt 220.5pt 257.25pt 294.0pt 330.75pt 367.5pt
404.25pt 441.0pt 477.75pt 514.5pt 551.25pt 588.0pt 624.75pt
661.5pt 698.25pt 735.0pt 771.75pt 808.5pt 845.25pt 882.0pt
918.75pt 955.5pt 35.0cm 1029.0pt 1065.75pt 1102.5pt 1139.25pt
1176.0pt;
mso-layout-grid-align:none;text-autospace:none">
<span style="font-size:9.0pt;
font-family:"Courier
New";mso-ansi-language:EN-US;mso-fareast-language:EN-US"><span
style="mso-spacerun:yes">
</span>6<span style="mso-spacerun:yes"> </span>7<span
style="mso-spacerun:yes">
</span>1 </span></p>
<br>
I could not see " _ " using vi in my topology. However, when I
copied all topology to another text editor I could. Then
removing it solves the problem. Is that a bug?
<br>
</div>
</blockquote>
<br>
Don't know - you haven't seen what you were doing when you observed
the weird behaviour. So far it sounds like someone has edited a file
with an editor that did not save plain text, since "20" is
hexadecimal for 32, which is the code for a space character, and
maybe some other weird character got rendered with "_".<br>
<br>
Mark<br>
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