[gmx-users] positional restraint
spoel at xray.bmc.uu.se
Tue Nov 30 18:48:28 CET 2004
On Tue, 2004-11-30 at 17:12 +0100, Xavier Periole wrote:
> David wrote:
> >On Tue, 2004-11-30 at 01:32 +0530, Alok wrote:
> >>hello David and Xavier,
> >> Thanks for all your responses to my previous
> >>mails.I am sorry,I still have to bother you with
> >>some more queries about the constraint.In the
> >>process i would also like to answer few questions
> >>u have asked in your responding mails.
> >>What is the range of differences you observe ?? Is it for the restrained
> >>part or the rest of the protein ?
> >>The Observed distance difference is for the restrained part (the atoms
> >>from the constrained residue).I have not checked the distance difference
> >>between the other atoms of the protein as i expect it to vary anyway since
> >>i am constraining only one residue in my protein.
> >>I present below data of distances (in Angstrom) between atoms of my
> >>constained residue for the crystal structure as well as for the output
> >>after Energy minimization using different Force constant.
> >> (Force Constant)
> >> Crystal 1000 10000 100000
> >> O-OD1 2.58 3.17 2.87 2.66
> >Is your OD1 protonated? It should...
> It seems to me that this residue is a ASN, since it contains OD1 and
> ND2. So I do not see why
> the OD1 should be protonated. I must be missing something !
> Although the distance is really small and should be a H-bond, which
> explain certainly why David
> suggested that the OD1 should be protonated. That is my guess.
> Another solution is that the X-ray attributed the density of ND2 to OD1
> and vis versa, That happens
> as the two atoms a not nesseraly easily discernable !
I had interpreted it as ASP, and the person who asked the question in
the first place confirmed that it was protonated.
Please double check! If it ASN then they should not be so close. If it
is ASP, and you don't protonate it they will also move apart.
Supply more information in the future please!
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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