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Hello Hau--
>
> I am trying to calculate the structure of my peptides containing HYP residues
> and I have been searching around for a topology and parameter file for HYP. I
> had copied topology file for Proline and modify to add -OH group but I've
> always got error messages such as
>
> %PATCH-ERR: angle -C +N +HN not found
> %PATCH-ERR: improper +HN +N -C -CA not found
>
> I modified the file ops.topology to rename the H atom to HN but still had the
> same error.
>
> I also have the other errors:
>
> %CODANG-ERR: missing angle parameters %%%%%%%%%%%%%%%%%%%%%%%%
> angle energy constant missing.
> target angle value missing.
> ATOM1: SEGId=" ", RESId="6 ", NAME="CB ", CHEMical="CT "
> ATOM2: SEGId=" ", RESId="6 ", NAME="CG ", CHEMical="CP "
> ATOM3: SEGId=" ", RESId="6 ", NAME="OD1 ", CHEMical="OH "
>
> I'm wondering if you have constructed the standard topology and parameter
> files for HYP that you could please share with me. Thank you so much for your
> help.
>
This has been asked before, and I am posting a response to the mailing
list to share the results with others. I'm attaching a script which
includes the necessary residue topology and parameters statements
in addition to the necessary invocation of the old XPLOR SEGMent
statement to generate the PSF. Use of the HYP residue requires a
modification of the linkage specification- and we'll update the Python
interface to better handle this in an upcoming release.
Here the sequence is that of the ALA HYP ALA tripeptide. In any
follow-on calculations, the updated parameters below will be required.
The parameters for the residue are approximate, but I believe I have
the correct chirality for the CG center.
best regards--
Charles
genHYP.py
Description: Binary data
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