Hello,
I'm having problems with the chirality.c module. It's kinda hard to explain the exact conditions that give rise to the error without getting too technical, but basically I'm using a custom residue with custom atom types. This residue is effectively arginine with three extra hydrogens, HZ1, HZ2 and HZ3 (almost exactly) superimposed onto NE, NH1 and NH2 and bonded to CZ. This causes chirality.c to give an error and crash LEaP if the pdb containing this residue is loaded. This doesn't happen if CZ has any two bonds fewer or if, bizarrely, N is not designated as the head atom of the residue.
This gives the following error:
ERROR: Comparing atoms
.R<VXI 1>.A<NE 14>,
.R<VXI 1>.A<HZ1 17>,
.R<VXI 1>.A<HZ2 18>, and
.R<VXI 1>.A<HZ3 19>
to atoms
.R<VXI 1>.A<NH1 20>,
.R<VXI 1>.A<NE 14>,
.R<VXI 1>.A<HZ3 19>, and
.R<VXI 1>.A<HZ1 17>
This error may be due to faulty Connection atoms.
!FATAL ERROR----------------------------------------
!FATAL: In file [chirality.c], line 142
!FATAL: Message: Atom named NH1 from VXI did not match !
!
!ABORTING.
The thing is, I've been working with custom residues for years, some with similar geometries and C with 6 bonds, and I've never encountered this particular error.
I have a few questions about this situation: what does the chirality.c file calculate and do? What is causing it to give an error exactly? And why is the residue head relevant in this circumstance?
Suffice to say, the conditions that I'm using are necessary for my purposes, and therefore I need to find a way to work them in.
If anyone has any clue as to what chirality.c does, that'd be helpful.
Cheers
Pietro
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Received on Fri Sep 04 2015 - 08:30:02 PDT
