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 Fri Oct 07 2016 - 15:00:03 PDT
