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

Justin Lemkul jalemkul at vt.edu
Fri Dec 14 20:34:00 CET 2012

On 12/14/12 2:28 PM, James Starlight wrote:
> Today I've tried to rename atoms from Swiss's params specific names to
> the standard charmm names and obtain the set of the same errors
> No default Improper Dih. types
> No default U-B types
>   No default Bond types
> Its strange to me because chromophore itself consist of only one
> uncommon bond  (in cyclized ring which could produce only several
> additional angles and dihedrals)
> By comparison in the case of Swiss atom names the total amount of the
> same errors was only 9 (all erors about unknown dihedrals with
> theadjacent residues. Although I've added capes in that model which
> mimicks adjacent residues) it's difficult recognize suitable dihedral
> types.
> Do you know any others attemps to simulate GFP with chromophore in
> charmm with proof parameters ?

This was linked before, at least once:


The authors provide parameters for everything you need.  We used these several 
years ago.



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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