On Wed, Oct 19, 2016, Thakur, Abhishek wrote:
>
> > antechamber -i PLX4720.pdb -fi pdb -o PLX4720.mol2 -fo mol2 -c bcc -s 2
> But It was continuously giving me error
> ---Judge bond type for Residue 1 with ID of 1 and Name of GLU ---
>
> ---Judge bond type for Residue 2 with ID of 2 and Name of ASN ---
>
> Warning: the assigned bond types may be wrong, please :
> (1) double check the structure (the connectivity) and/or
> (2) adjust atom valence penalty parameters in APS.DAT, and/or
> (3) increase PSCUTOFF in define.h and recompile bondtype.c
> Be cautious, use a large value of PSCUTOFF (>100) will significantly increase the computation time
Note: antechamber is intended for *small molecules*, not for polypeptides or
proteins. Amber builds proteins in a completely different way: please see the
manual or tutorials.
[Scott: does acdoctor properly complain if a user tries to use a protein pdb
file?]
...good luck...dac
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Received on Wed Oct 19 2016 - 17:30:02 PDT
