<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><DIV>After checking the topology of my peptide, I found that every term in the cMAP section involve three consecutive residues. So I guess no cMAP term is required for di-ALA. </DIV>
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<DIV>Jianguo<BR></DIV>
<DIV><BR>--- On <B>Mon, 10/10/11, César Ávila <I><clavila@gmail.com></I></B> wrote:<BR></DIV>
<BLOCKQUOTE style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: rgb(16,16,255) 2px solid"><BR>From: César Ávila <clavila@gmail.com><BR>Subject: Re: [gmx-users] CMAP for alanine dipeptide in Charmm27 ff<BR>To: "Jianguo Li" <ljggmx@yahoo.com.sg>, "Discussion list for GROMACS users" <gmx-users@gromacs.org><BR>Date: Monday, 10 October, 2011, 5:51 PM<BR><BR>
<DIV id=yiv734092412>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=yiv734092412gmail_quote>2011/10/10 Jianguo Li <SPAN dir=ltr><<A href="http://sg.mc781.mail.yahoo.com/mc/compose?to=ljggmx@yahoo.com.sg" target=_blank rel=nofollow ymailto="mailto:ljggmx@yahoo.com.sg">ljggmx@yahoo.com.sg</A>></SPAN><BR>
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<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>
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<B><SPAN style="FONT-WEIGHT: bold">From:</SPAN></B> César Ávila <<A href="http://sg.mc781.mail.yahoo.com/mc/compose?to=clavila@gmail.com" target=_blank rel=nofollow ymailto="mailto:clavila@gmail.com">clavila@gmail.com</A>><BR><B><SPAN style="FONT-WEIGHT: bold">To:</SPAN></B> Discussion list for GROMACS users <<A href="http://sg.mc781.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" target=_blank rel=nofollow ymailto="mailto:gmx-users@gromacs.org">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=yiv734092412im><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><FONT color=#888888>-- <BR>gmx-users mailing list <A href="http://sg.mc781.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" target=_blank rel=nofollow ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR><A href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target=_blank rel=nofollow>http://lists.gromacs.org/mailman/listinfo/gmx-users</A><BR>Please search the archive at <A href="http://www.gromacs.org/Support/Mailing_Lists/Search" target=_blank rel=nofollow>http://www.gromacs.org/Support/Mailing_Lists/Search</A> before posting!<BR>Please don't post (un)subscribe requests to the list. Use the <BR>www interface or send it to <A
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