[gmx-users] PYP chromophore force field
Mark.Abraham at anu.edu.au
Thu Apr 21 02:27:47 CEST 2011
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?
> [ 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.
> 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
> > --
> > gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 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
> (205) 690-0808 <tel:%28205%29%20690-0808> |
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users