Hi Xplor users,
I tried to use addAtoms.py with XplorNIH 2.19 to add 11 MTSL groups to a 183
residue protein and got the following:
Traceback (most recent call last):
File "stdin", line 1, in ?
File "addAtomsdsbb4.py", line 47, in ?
protocol.fixupCovalentGeom(sel=fixGeom)
File "/home/spincity/xplornih/xplor-nih-2.19/python/protocol.py", line
1408, in fixupCovalentGeom
raise CovalentViolation(mess)
protocol.CovalentViolation: Covalent geometry still violated after
fixupCovalentGeom
(violations: bond: 0 angle: 0 improper: 5)
Try increasing maxIters or enabling the useVdw flag.
I changed protocol.fixupCovalentGeom(sel=fixGeom) to
protocol.fixupCovalentGeom(,maxIters=1000,useVDW=1) but
when I reran addAtoms.py I got an error similar to that above. I changed
maxIters to 5000, reran addAtoms.py
and got the same error as previously.
Next I used the same addAtoms.py as in my initial attempt above with
XplorNIH 2.18 and got pdb and psf files and no error message. The pdb file
did have several MTSL geometry errors. I used this file as input for an
annealing and energy minimization procedure very similar to
eginput/prot_prot/sa_cross_tor.inp with no experimental restraints. The
output pdb file contained no MTSL geometry errors.
My questions are:
1. Is there something other than what I did above that can be tried to
get correct geometry when using addAtoms.py with XplorNIH 2.19?
2. Is there any way to get pdb and psf file output from addAtoms.py
with XplorNIH 2.19 instead of an error message even if the geometry is not
correct?
3. Is there a way to make the addAtoms.py geometry correction more
robust? If yes, what is the best approach?
Thanks,
Jeff Ellena
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