[Xplor-nih] patch-err when using seq2psf with HYP residue added

[Charles at Schwieters.org]

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Hello Fred--

> I have added hydroxyproline parameters to the protein.par and
> protein.top files and have added 'HYP' to the residue types in
> psfGen.py 
> When I use seq2psf I get the following errors:
> 
>  %PATCH-ERR: angle -C    +N    +HN   not found 
>  %PATCH-ERR: improper +HN   +N    -C    -CA   not found
> 
> The program still creates the PSF file, but I was curious as to the
> patch-err. 
> 

The HYP residue type is defined in the opls topology file. This file
does not follow Xplor-NIH atom naming conventions. In particular, the HN
atom is named H. The result here is that a peptide angle and improper
are missing in your psf. One solution would be to rename the H atom to
HN.

best regards--
Charles

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