On Mon, Aug 02, 2010, Francesca Cantini wrote:
>
> I would like to ask you how can I convert the upl constraints of
> cyana of QE and/or QD of TYR and PHE residues in amber format. I have
> seen that in the file map.DG-amber there is only QB or QD for the
> geminal protons but in the case of TYR or PHE there aren't QE or QD.
I'm lost here: map.DG-AMBER certainly has QD and QE entries for PHE and TYR;
for example:
RESIDUE PHE
MAPPING O = O
MAPPING N = N
MAPPING HN = H
MAPPING HA = HA
MAPPING HB2 = HB2
MAPPING HB3 = HB3
MAPPING QPB = HB2 HB3
MAPPING QB = HB2 HB3
MAPPING HD = HD1 HD2
MAPPING CG = HD1 HD2
MAPPING HE = HE1 HE2
MAPPING CZ = HE1 HE2
MAPPING HZ = HZ
MAPPING QD = HD1 HD2
MAPPING QE = HE1 HE2
The last two lines say that the "QD" resonance is HD1 plus HD2, which are
interchanging fast enough to appear as only one resonance in the spectrum;
this is appropriate for most PHE residues in proteins. The are not treated
as geminal protons.
...hope this helps....dac
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Received on Mon Aug 02 2010 - 17:00:03 PDT
