[gmx-users] more questions

Luke Czapla czapla at rutchem.rutgers.edu
Tue Oct 9 03:14:58 CEST 2001

On Mon, 8 Oct 2001, David van der Spoel wrote:

> There may be a simpler way. If you just have a single bond between the two
> residues you can add it to the specbond database. pdb2gmx will then look
> for Ser-Gly combinations in bonding distance. So what is the chemical
> nature of the link?

Hi David,
  The carbonyl of serine 65 forms a bond to the amino group of glycine 67
forming an imidazole ring and the alpha-beta carbon bond of tyrosene 66 is
oxidized to a double bond.  The result is a highly conjugated planar
structure.  My guess is that it will not be simple to implement, but with 
some guidance on how to modify the .rtp and other necessary files I could 
post a preliminary definition for this chromophore.  Thank you for your


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