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Hello--
>
> First, in the anneal.inp for protG, the coefficients of SANI are :
> ---------------------------------
> coeff 0.0 -9.9 0.23
> @bicelles_new_nh.tbl {* dipolar coupling restraints for protein
> amide NH. *}
> end
> -----------------------------------
> I think this means Da=-9.9 and R=0.23. But as I know,
> Da = 0.5 * D(max), D(max) : the maximun value of the residual dipolar
> coupling
> So Da of NH vector should be positive. Why you use -9.9 ???
in the notation of Bax, Kontaxis, and Tjandra, Methods in Enzymology
399, 127 (2001):
Da = 0.5 * D(max) * Aa
where Aa is the axial part of the alignment tensor, and can be negative.
> AT_Build::buildNode: cycle link found between atoms 13 PCA 1 CD and 1
> PCA 1 N
> removing bond.
> AT_Build::buildNode: cycle link found between atoms 328 CYS 19 C and
> 322 CYS 19 CA
> removing bond.
> AT_Build::buildNode: cycle link found between atoms 1110 CYS 68 C and
> 1104 CYS 68 CA
> removing bond.
> AT_Build::buildNode: cycle link found between atoms 1414 CYS 87 C and
> 1408 CYS 87 CA
> removing bond.
> AT_Build::buildNode: cycle link found between atoms 786 CYS 48 CB and
> 782 CYS 48 CA
> removing bond.
> MAKINB: mode 4 found 9478 exclusions, 0 interactions(1-4) and
> 5134 GB exclusions
> ---------------------------------------------------------------------------
> PCA means pyroglutamate. The bonds which are removed are actually exist.
> Why remove them??
The bonds are still there - in the force field, but they have been
removed by the IVM engine because they form topological cycles, which
are not allowed.
Most frequently in proteins, cycles occur in regions of aromatic
sidechains which should remain rigid- and these are handled by the
anneal.inp script. The PCA residue seems to have an internal loop- but
the script knows nothing about this- what does this residue look like?
You also seem to have disulfide bonds, which you probably should break
explicitly (again topologically- bond forces remain) using BREAk
statements within the IVM. For instance, one statement might look like
this:
break (resid 19 and name S) (resid 87 and name S)
I'm sure the residue numbers are incorrect for your case.
> And there are 8 CYS residues in my protein, but only 4 of
> them have this phenomena.
> Is this important ????
8 CYS residues probably means 4 disulfide bonds to break.
regards--
Charles
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