On Tue, Aug 27, 2013, glbala87.imtech.res.in wrote:
>
>
> bala.bala-desktop:~/Desktop$ /home/bala/Tools/amber11/exe/antechamber -i
> plp_new.pdb -fi pdb -o plp.mol2 -fo mol2 -c bcc -s 2
> Running: /home/bala/Tools/amber11//bin/bondtype -j full -i
> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
>
> Warning: the assigned bond types may be wrong, please :
Most of the time the problem is with the input structure (in the plp_new.pdb
file). Make sure it looks good visually, is a reasonably small molecule (MW
less than 1000 or so) and has all its hydrogen atoms.
If you can't find any problems, you can try using the -j command to
antechamber to relax the bond checking.
...dac
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Received on Tue Aug 27 2013 - 06:30:04 PDT
