On Mon, Sep 26, 2016, shahab shariati wrote:
>
> I'm really confused. I used antechamber for 5 other ligands without any
> problems.
Remove the CONECT cards from the lig.pdb file. These cards have many, many
repeated entries; looking at just the top few here:
CONECT 1 38 46 64
CONECT 2 3
CONECT 2 3
CONECT 2 3
CONECT 2 3
CONECT 2 14
CONECT 2 14
CONECT 2 14
CONECT 2 14
CONECT 2 65
CONECT 3 2
CONECT 3 2
CONECT 3 2
CONECT 3 2
CONECT 3 4
CONECT 3 4
CONECT 3 4
CONECT 3 4
CONECT 3 66
CONECT 4 3
CONECT 4 3
CONECT 4 3
CONECT 4 3
I'm not sure if it is the duplicated entries, or errors in the
connectivity that is the problem, but they are confusing antechamber,
which should work OK after the change.
Note: running the "acdoctor" program on troublesome input is highly
recommended:
acdoctor -i lig.pdb -f pdb
In the next release, antechamber will automatically run acdoctor to try to
identify problems, and give more helpful error messages.
....dac
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Received on Mon Sep 26 2016 - 18:30:03 PDT
