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

Justin Lemkul jalemkul at vt.edu
Wed Dec 12 13:46:45 CET 2012

On 12/12/12 6:54 AM, James Starlight wrote:
> Oh that problem was imperically resolved by renamind O2 ( which are
> not terminal but pdb2gmx define them as a terminal ) atom to O3
> The only question about my chromophore is the definition of the IMPROPER groups.
> As I've posted above my initial model was CAPPED from C and N termi by
> NH2 and Ace. The resulted topology consisted of Improper for bonds
> between chromophore atoms and Capped groups ( e.g :
> With ACE (C-3 O-1 C-4 H-11 H-12 H-1 )
> IMPH C    N1   CA3  O
> IMPH N    C3   CA1  H11
> IMPH C3   O1   N    C4
> IMPH C4   HC11 C3   H1
> IMPH C4   HC11 C3   H12
> With NH2  (N1-H2-H3)
> IMPH N1   H2   C    H3
> IMPH C    N1   CA3  O
> That strings were removed from chromophore RTP. But in my final model
> there are 2 amino acids insted of capped groups so the IPROPERS must
> be inclusion for protein-chromophore nonds. How it could be done ?
> In some amino acids I've found -N and -C blocks that (if I understood
> correctly) for C and N atoms of the adjacent residues. How that atoms
> must be defined correctly in the protein-chromophore comples ?

+ and - indicate next and previous residues, respectively.  Presumably your 
chromophore engages in the same types of peptide bonds as any other amino acid, 
so the syntax is the same as any other case.



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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