Hello,
I am trying to use implicit water refinement methods to help clean up some
torsional issues with my head to tail cyclic peptides; the sequences are a mix
of D- and L- amino acids and a few also contain disulfide linkages.
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?
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 am wondering if there is an issue with using the LtoD patches with the eefx
force fields or is there something else I am doing wrong? I have tried to load
the refine.sa structures directly into the refine_eefx.py script without
generating new .psf files, however this just gives me an error of missing atoms
for the first and last residues which are linked by head to tail cyclization
and script fails with a SystemError message:
SystemError: xplor-nih error: error reading restraint: selection string resid
1 and name HN selects no atoms
PyInterp::command: error executing: >execfile('refine2_eefx.py')<
NOTE: I am using xplor-nih-2.45 on Ubuntu.
Thank you for any input
Take care,
Matt
___________________________
Matthew D. Shortridge, PhD
Research Associate
University of Washington
Department of Chemistry
http://depts.washington.edu/varani2/
_______________________________________________
Xplor-nih mailing list
[email protected]
https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
