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On 13/10/2011 8:16 PM, Ahmad Randy wrote:
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cite="mid:1318497379.77359.YahooMailNeo@web161720.mail.bf1.yahoo.com"
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<div id="yiv1838999723yui_3_2_0_18_1318493452496112"
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style="font-family: times new roman,new
york,times,serif; font-size: 12pt;">Hi All,<br>
<br>
I understand that there were already some discussions
about new DSSP exec with do_dssp in gromacs-4.5.4. I
just want to make clear, is it true that this two DSSP
and do_dssp do not compatible each other? <br>
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<br>
If the new DSSP requires the code in do_dssp to be updated, that
hasn't happened, and likely won't happen for a while. If someone can
substantiate that it needs a change, and file a GROMACS Redmine
issue describing what needs to happen, then it will be considered
for the 4.6 release.<br>
<br>
<blockquote
cite="mid:1318497379.77359.YahooMailNeo@web161720.mail.bf1.yahoo.com"
type="cite">
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255); font-family: arial,helvetica,sans-serif; font-size: 12pt;">
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255, 255); font-family: arial,helvetica,sans-serif;
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<div id="yiv1838999723yui_3_2_0_18_1318493452496112"
class="yiv1838999723yui_3_2_0_18_131849345249683"
style="font-family: times new roman,new
york,times,serif; font-size: 12pt;"><br>
I was running in Ubuntu 10.04, and this is what I got:<br>
<br>
<span id="yiv1838999723yui_3_2_0_18_1318493452496184"
class="yiv1838999723tab"> </span><span
id="yiv1838999723yui_3_2_0_18_1318493452496189"
class="yiv1838999723tab"> </span><span
id="yiv1838999723yui_3_2_0_18_1318493452496194"
class="yiv1838999723tab"> </span>do_dssp -f
300K.trr -s 300K.tpr -o dssp<br>
<br>
I choose 5 'Mainchain'<br>
<br>
<span class="tab"> </span><span class="tab"> </span><span
class="tab"> </span>Fatal error:<br>
<span class="tab"> </span><span class="tab"> </span><span
class="tab"> </span>Failed to execute command:
/home/madndy/dssp/dssp -na ddkbeHeQ ddvDjL4J >
/dev/null 2> /dev/null<br>
<br>
<br>
I already set the "export DSSP=/home/madndy/dssp/dssp",
and also try the latest do_dssp.c (from gromacs-4.6)
file for instalation. Still didn't work.<br>
<br>
Are there are any suggestion or correction in my step?
Or what version of gromacs that work well with DSSP? Or
should I get the older version of DSSP that work with
do_dssp? </div>
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<br>
I think that is the most reliable approach.<br>
<br>
<blockquote
cite="mid:1318497379.77359.YahooMailNeo@web161720.mail.bf1.yahoo.com"
type="cite">
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255); font-family: arial,helvetica,sans-serif; font-size: 12pt;">
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<div style="color: rgb(0, 0, 0); background-color: rgb(255,
255, 255); font-family: arial,helvetica,sans-serif;
font-size: 12pt;">
<div id="yiv1838999723yui_3_2_0_18_1318493452496112"
class="yiv1838999723yui_3_2_0_18_131849345249683"
style="font-family: times new roman,new
york,times,serif; font-size: 12pt;">And where can I find
the older version of DSSP because I can't find the older
version in: <a class="moz-txt-link-freetext" href="http://swift.cmbi.ru.nl/gv/dssp/">http://swift.cmbi.ru.nl/gv/dssp/</a> . <br>
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<br>
They say it is available. Please ask them.<br>
<br>
Mark<br>
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