Dear Amber Users,
While using the conversion command described in RED manual, pp 15, I
found a bug. The following command converts a pdb file not having
connection information to a pdb file that will have the connection
informations.
babel -ipdb unconnected_pdb.pdb -opdb connected_pdb.pdb
The output of the connected_pdb.pdb cannot be read in MOLDEN program. (Did
not use Insight 2 whetehr it can read it or not) The error can be solved
in the following way:
connected_pdb.pdb (the file which cannot be read by MOLDEN)
ATOM 1 O5' C 14 5.422 28.232 13.133 1.00 0.00
ATOM 2 C5' C 14 3.994 28.337 12.977 1.00 0.00
....
delete a line left to the 'C' while keeping the column with the name
'14' in its original place, such as,
ATOM 1 O5' C 14 5.422 28.232 13.133 1.00 0.00
ATOM 2 C5' C 14 3.994 28.337 12.977 1.00 0.00
Best,
--
Ilyas Yildirim
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Received on Tue May 25 2004 - 19:53:00 PDT
