[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

Justin Lemkul jalemkul at vt.edu
Sun Dec 16 17:12:35 CET 2012

On 12/16/12 10:34 AM, James Starlight wrote:
> Justin,  thanks again for explanation.
> So the first 5 atoms in cmap.it correspond to the starting sequence of
> the backbone atoms of the amino acid doesnt it ? So what is the  24 24
> numbers at the end of each cmap line ?

Probably something related to how Gromacs tools read in the CMAP data.  I don't 
have time to go through the code to find exactly how it's used.

> E.g in the  C NH1 CT1 C NC=O 1 24 24\ the first C B CA C N atoms would
> be assigned as the backbone. That lines were added after grompp
> produce error about unknown cmap for that 5 atoms of the chromophore.
> Should the 24 24 \ be removed from each line of the chromophore cmap ?

You shouldn't be modifying anything about cmap.itp, nor should those numbers be 
present in your .rtp file.  Your [cmap] directive in the .rtp entry should 
contain a sequence of 5 atom names to which the CMAP corrections are applied.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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