Hello,
Using the bondbydistance command I have found a workaround. I load the lib as normal, with all the correct bonds I intend to have, except the N of the custom residue is not designated as the head atom. Upon loading the lib and pdb, there is no error, save for the fact that the custom residue is not bound on the N-side. The bondbydistance command rectifies this and there is no problem. It's an extra step and it's clunky, but it works so far, so thank you for suggesting it.
My question still stands, however: what does chirality.c do? What causes it to give an error? Why is it dependant on the status of the head atom of the residue, if it gives errors using completely different atoms?
Cheers
Pietro
-----Original Message-----
From: David A Case [mailto:david.case.rutgers.edu]
Sent: 05 September 2015 17:14
To: AMBER Mailing List
Subject: Re: [AMBER] chirality.c
On Fri, Sep 04, 2015, Aronica, Pietro wrote:
> 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.
What happens if you load the residue as a PDB file (with no connectivity), use the "bondbydistance" command, and save as an off or mol2 file?
If this doesn't help, I think we would need to know details about how you constructed the residue. At least, the actual structure files, rather than just a description in words.
....dac
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Received on Tue Sep 08 2015 - 07:30:03 PDT
