Hi Yusuf
thanks for your report. This bug is fixed in our development code.
Cheers.
Hai
On Fri, Oct 7, 2016 at 5:37 PM, Yusuf Simsek <simsek.ualberta.ca> wrote:
> Dear AMBER developers,
>
> I would like to report a bug in pdb4amber code (AmberTools16)
>
> Bug is related to finding gaps between consecutive C-alpha atoms in
> residues.
>
> File: pdp4amber
> Location: { amber16/AmberTools/src/amberlite/pdb4amber05/pdb4amber }
> or { amber16/bin/pdb4amber }
>
> Function Name: def find_gaps(recordlist):
>
> Function Line Number: 694
>
> -------------------------------------------
> for i in range(nca-1):
> if is_ter(ca_atoms[i]):
> continue
> ca1 = recordlist[ca_atoms[i]]
> ca2 = recordlist[ca_atoms[i+1]]
> dx = float(ca1[11]) - float(ca2[11])
> dy = float(ca1[12]) - float(ca2[12])
> dz = float(ca2[13]) - float(ca2[13]) <---- Error (line number 725)
> gap = sqrt(dx*dx +dy*dy +dz*dz)
> ---------------------------------------------
>
> Both elements of subtraction are written as c2[13], one of them should be
> c1[13].
>
> float(ca2[13]) - float(ca2[13]) --> produce 0.0 value everytime.
>
> dz = float(ca2[13]) - float(ca2[13]) should be like dz = float(ca1[13]) -
> float(ca2[13])
>
>
> Thanks,
>
> Yusuf Simsek
>
> Department of Chemistry
> University of Alberta
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Received on Sat Oct 08 2016 - 10:30:02 PDT
