[gmx-users] CMAP for alanine dipeptide in Charmm27 ff

[Jianguo Li]

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. 
 
Jianguo


--- On Mon, 10/10/11, César Ávila <clavila at gmail.com> wrote:


From: César Ávila <clavila at gmail.com>
Subject: Re: [gmx-users] CMAP for alanine dipeptide in Charmm27 ff
To: "Jianguo Li" <ljggmx at yahoo.com.sg>, "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Monday, 10 October, 2011, 5:51 PM


v4.5.4 
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. 
Cheers
Cesar


2011/10/10 Jianguo Li <ljggmx at yahoo.com.sg>




which gromacs version are you using? cMAP is implemented in v4.5  or later

Jianguo






From: César Ávila <clavila at gmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Sunday, 9 October 2011 12:07 AM
Subject: [gmx-users] CMAP for alanine dipeptide in Charmm27 ff



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? 


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