Dear Sir :
I have two questions about structure refinement against RDC !!
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 ???
Second Question :
I use the input file, anneal.inp, to refine the structures with residual
dipolar coupling following
the procedure published on JMR(1998) 131, page151-162.
Then I saw the following messages in the output file.
-----------------------------------------------------------------------
X-PLOR> dynamics internal
Internal Dynamics> timestep $timestep
Internal Dynamics> endt 3
Internal Dynamics> tbath $bath
Internal Dynamics> nprint $nstep
Internal Dynamics> ntrfr 1
Internal Dynamics> end
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?? And there are 8 CYS residues in my protein, but only 4 of
them have this phenomena.
Is this important ????
I am looking forward to your reply. Thanks a lot!!!!!
Best regards,
Yuan-Chao Lou
Postdoctoral fellow
Inst. of Biomedical Sciences
Academia Sinica, Taiwan.
E-mail : [email protected]
