Dear all,
I have 2 cis-prolines (as judged from chemical shifts and NOE
connectivities) in my structure.
I included a cipp-patch (for implementing cis-settings) in the
generate_seq.inp, but despite of this the mtf-file that was generated is
identical (apart from the file names) with the mtf-file which was
generated without the cipp-patch. >> although the cipp-patch was used
(but didn't actually effect any change of the mtf-file) the
subsequently generated pdb-file and the calculated ensemble obviously
came out trans.
It appears to me that the problem lies in generating the right (cis)
mtf-file.
For the above mentioned steps we used the following parameter and
topology files:
topallhdg5_3.pro
parallhdg5_3.pro
When I have used some older topology and parameter files (=
protein-allhdg_dih_ucl.top and protein-allhdg-ucl.param) and implemented
the cipp-patch, the structures came out cis and were alright.
However, in our lab the water-refinement step relies on
(parallhdg5_3.pro) and I run into problems using the ensemble calculated
with protein-allhdg-ucl.param.
If you have any comments or suggestion on how to overcome this issue, I
would be most thankful!
Thank you,
Christoph
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
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