[gmx-users] PYP chromophore force field

Peter C. Lai pcl at uab.edu
Thu Apr 21 01:57:05 CEST 2011

Isn't the chromophore supposed to be covalently bonded to the protein?
My cursory search shows Vengris et al 2004 in Biophys. J. citing Baca et al
1994 and van Beeumen et al 1993: "This small 125-residue protein contains a
p-coumaric acid chromophore that is covalently bound to the protein backbone
via a thiol-ester cysteine linkage Cys-69"...

Maybe you forgot to specify a covalent bond in your topology...

On 2011-04-20 06:46:54PM -0500, Ramachandran G wrote:
> Hi gromacs users,
>      I am working on Photo active yellow protein.
>     Although i successfully build the force field and patched the chromophore to the protein.
> After energy minimizing the protein, the chromophore flies away separately. I don't know whether i am missing anything?
> Please help.
> Rama

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Peter C. Lai                 | University of Alabama-Birmingham
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