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On 11/10/2011 4:51 AM, César Ávila wrote:
<blockquote
cite="mid:CAKz=r7JwwUjnA1L_=7ZRgyDih2tKvKqxUyCLxz7KTD+WB3kg8g@mail.gmail.com"
type="cite">v4.5.4 <br>
As I commented above, I had to manually add an entrance for the
cmap terms in the topology file as pdb2gmx would not generate them
for the alanine dipeptide. There seems to be no problem for larger
peptides. <br>
Cheers<br>
Cesar<br>
<br>
</blockquote>
<br>
That sounds like a bug. Please describe your symptoms in a new issue
here - <a href="http://redmine.gromacs.org/">http://redmine.gromacs.org</a><br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAKz=r7JwwUjnA1L_=7ZRgyDih2tKvKqxUyCLxz7KTD+WB3kg8g@mail.gmail.com"
type="cite">
<div class="gmail_quote">2011/10/10 Jianguo Li <span dir="ltr"><<a
moz-do-not-send="true" href="mailto:ljggmx@yahoo.com.sg">ljggmx@yahoo.com.sg</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div>
<div
style="color:#000;background-color:#fff;font-family:times
new roman, new york, times, serif;font-size:12pt">
<div><span>which gromacs version are you using? cMAP is
implemented in v4.5 or later<br>
</span></div>
<div>
<span>Jianguo<br>
</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"><font face="Arial"
size="2">
<hr size="1">
<b><span style="font-weight:bold">From:</span></b>
César Ávila <<a moz-do-not-send="true"
href="mailto:clavila@gmail.com" target="_blank">clavila@gmail.com</a>><br>
<b><span style="font-weight:bold">To:</span></b>
Discussion list for GROMACS users <<a
moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org"
target="_blank">gmx-users@gromacs.org</a>><br>
<b><span style="font-weight:bold">Sent:</span></b>
Sunday, 9 October 2011 12:07 AM<br>
<b><span style="font-weight:bold">Subject:</span></b>
[gmx-users] CMAP for alanine dipeptide in Charmm27
ff<br>
</font>
<div class="im">
<br>
<div>I would like to run REMD simulations on the
alanine dipeptide using the Charmm27ff + CMAP.
Still, after processing the pdb with pdb2gmx, I do
not see any entrance referring to the cmap term in
the topology file. Does this mean that Cmap won't
be calculated? <br>
<br>
</div>
<br>
</div>
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