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

Justin Lemkul jalemkul at vt.edu
Wed Dec 12 21:27:51 CET 2012

On 12/12/12 3:11 PM, James Starlight wrote:
> Justin,
> That errors was strange to me because I've already used Swiss's ITP
> files for diffusional ligands including them in the topol.top of my
> protein and there were no such errors about non-standart types in any
> terms. It seems that some additions to the ffbonded.itp also required
> besides the nonbonded.itp so the renaming Swiss's atoms to the CHARMM
> would be less routinelly. I noticed some atoms types in the paper
> which you provide me ( simulation in charmm22). Does the atom types
> similar in both charmm fieds?

You probably don't get any errors because the .itp files provided to you from 
the server include atomtype and bonded parameter definitions that are internally 
self-consistent.  What you're trying to do is use the "standard" CHARMM27 force 
field with some new molecule that has no guarantee to be fully defined under the 
existing force field.

CHARMM22 and CHARMM27 are the same for protein parameters, with the exception of 
the introduction of CMAP in the latter.

> Also I could not find any suitable example of CMAP for the long
> molecule like my chromophore. I noticed that for amino acid typical
> CMAP is the its backbone atoms as well as N and C atoms of 2 djacent
> residues. So does the CMAP for chromophore consist of 2 strings like
> below example or just one long strig ?
> [ cmap ]
> -C  N  CA1  C1  N2
> CA2 C2 N3 CA3 C

The proper approach would be separate strings of 5 atoms.



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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