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

Justin Lemkul jalemkul at vt.edu
Fri Dec 14 21:24:19 CET 2012

On 12/14/12 3:20 PM, James Starlight wrote:
> Justin,
> in the case of the system with the atom types assigned from that paper
> the grompp produced above 118 errors of non standard bond, angle as
> well as dihedral types ;o So it' seems that some 118 addition terms
> must be added to the ffbonded.itp to the existing charmm parameters(
> it's uncommon for me because in that case the atom names werefrom
> standart charmm ff but the total number of errors was bigger than in
> case of Swiss params non-standart names usage).

I'm not sure why there were so many errors when you used those parameters.  Like 
I said, we've used them before.  I recall a few errors along the way, but manual 
assignment of the bonded parameters according to the paper is fairly 

> By the way I've simulated choromophore produced by SWISS ( with the
> charges assigned from the paper) in the vacuum and didnt notice any
> inaccuracy in the conformation of chromophore. So the last that I
> should is the carefull assignment of the 9 missed dihedral terms with
> the rest of the protein.

Sounds like a reasonably approach.  Good luck.



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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