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><div class="gmail_quote">2011/10/10 Jianguo Li <span dir="ltr"><<a 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 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 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>
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