Hello Matt--
>
> I started this project using a set of legacy scripts which were
> handed down to me, they've worked well, but I've recently migrated
> to using the python based scripts from /eginput/gb1_rdc. Thus far
> I've been able to generate clean .psf files for my cyclic sequences
> and calculate structures using the anneal.py and refine.py scripts
> with little issues. As an added bonus, the python generated
> structures match well with legacy script structures.
>
> However, when I try to load the structures into the water refinement
> scripts (refine_eefx.py) I start having issues. From what I can
> tell, it appears I need to make new .psf files with the eefx force
> fields to load into these scripts?
That is correct.
> I first tried to do this by calling in the protein_eef.top &
> protein_eef.par force fields in the genCircpep.py script compared to
> the protein-3.1 versions. This approach appears to generate a
> cyclic peptide .psf file, however it appears to skip over LtoD
> patches with these force fields. With the LtoD patch turned on, the
> script fails at protocol.fixupCovalentGeom with the error. With the
> LtoD patch turned off I do not get this error.
>
> %CODIMP-ERR: missing improper parameters %%%%%%%%%%%%%%%%%%%%%
> improper energy constant missing.
> target improper value missing.
> periodicity missing.
> ATOM1: SEGId=" ", RESId="2 ", NAME="HA ", CHEMical="HB "
> ATOM2: SEGId=" ", RESId="2 ", NAME="C ", CHEMical="C "
> ATOM3: SEGId=" ", RESId="2 ", NAME="N ", CHEMical="NH1 "
> ATOM4: SEGId=" ", RESId="2 ", NAME="CB ", CHEMical="CT2 "
I do apologize. These parameters were missing from
toppar/eefx/protein_eefx2.par:
IMPRoper HB C NH1 CT1 500 {sd=0.031} 0 66.2535
IMPRoper HB C NH1 CT2 500 {sd=0.031} 0 66.1640
IMPRoper HB C NH1 CT3 500 {sd=0.031} 0 65.9907
I've placed a full version of the updated file here:
https://nmr.cit.nih.gov/out/protein_eefx2.par
Please copy this to the toppar/eefx directory under you Xplor-NIH
distribution.
Please let me know if you continue to have problems.
best regards--
Charles
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