[gmx-users] PYP chromophore force field

[Mark Abraham]

On 4/21/2011 10:12 AM, Ramachandran G wrote:
>
> Yes, you are right, the chromophore(p-coumaric acid) is covalently 
> bonded to the Sulphur(S) atom of the Cys-69 residue.
> But I specified the covalent bond in my topology.
>
> [ bonds]
>  C   +SG

That's your .rtp entry. What's in your [molecules] section of your topology?

Mark

>
> [ angles ]
>       O    C   +SG
>      CA1   C   +SG
>       C  +SG   +CB
>
> [ dihedrals ]
>       O     C  +SG    +CB
>      CA1    C  +SG    +CB
>      HA2   CA1   C   +SG
>      CA2   CA1   C   +SG
>       C   +SG  +CB   +CA
>       C   +SG  +CB   +HB1
>       C   +SG  +CB   +HB2
>
> After doing pdb2gmx, i got the right structure. But the chromophore 
> flies away after minimising.
>
>
> Thanks
> Rama
>
> On Wed, Apr 20, 2011 at 4:57 PM, Peter C. Lai <pcl at uab.edu 
> <mailto:pcl at uab.edu>> wrote:
>
>     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
>     Programmer/Analyst           | BEC 257
>     Genetics, Div. of Research   | 1150 10th Avenue South
>     pcl at uab.edu <mailto:pcl at uab.edu>                  | Birmingham AL
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