Hi every one
I have launched calculations with RDCs (two media, peg and phage) on my
protein. Since my protein has 4 modules, with some of them being mobiles,
I have used up to 8 tensors. (assuming every module was behaving
independently), or only 2 tensors (assuming that the protein is completely
rigid). All calculations converge, with more or less violations, but the
the calculations made under the rigid assumption. (not surprising). But my
problem is the following:
Numbering of my protein begins at 355 and finish at 626.
I have hence introduced the tensors in the pdbfile as ANI 700, ANI 701,
..., 707. (if necessary)
and in the RDC restraints filesas well. But I have the feeling that I may
have skipped something somewhere, and that the software hence still makes
calculations with tensors numbered 500, 501...
In the out file, I will have the following messages (I only write the one
corresponding to the tensor 700, but I have also the 7 others,(in the case
of the calculation with 8 tensors) with different numberings of course..)
:
calcTensorOrientation(media[medium])
AT_Build::buildNode: cycle link found between atoms 2141 VAL 500 C and
2143 ALA 501 N
removing bond.
*-- POWELL ------ step= 0 --- stepsize= 0.01000 --- energy evals=
2 -*
| E(poten)= 26362.5488668 grad= 3373.7631740 peg1_NH=
26362.5488668 |
*------------------------------------------------------------------------------*
*-- POWELL ------ step= 10 --- stepsize= 0.01000 --- energy evals=
24 -*
| E(poten)= 19189.7677656 grad= 2425.1536755 peg1_NH=
19189.7677656 |
*------------------------------------------------------------------------------*
Powell::step: normal exit.
*-- POWELL ------ step= 15 --- stepsize= 0.01000 --- energy evals=
10 -*
| E(poten)= 19189.7277415 grad= 2425.4538268 peg1_NH=
19189.7277415 |
*------------------------------------------------------------------------------*
refinement1234.py(165): rampedParams.append(
StaticRamp("calcTensor(media['%s'])" % medium) )
And more bothering for me, if I have a RDC restraint concerning residues
500, 501, 502 ... , the energies becomes incredibely high at the beginning
of the calculation.
Finally, I observed that for the calculations under the rigid assumption
(only two tensors, ANI 700 and ANI 701), the high level of energies was
due to residue 500 and 501 which were completely exploded.
Hence, I really have the impression that somewhere, I did something wrong
in the calculation.
All the protocol has been derived from the protocole for refinement of
protein G (tutorial).
Any help appreciated!
--
H?l?ne D?m?n?, PhD
Centre de Biochimie Structurale
UMR 5548 CNRS-UM1-INSERM UMR 554
29, rue de Navacelles
34090 Montpellier Cedex
France
Tel: +33 (0) 4 67 41 77 01
Fax: +33 (0) 4 67 41 79 13
e-mail: Helene.Demene at cbs.cnrs.fr
--
Passerelle antivirus CBS
