On Sat, Jun 24, 2017, Mustafa Alhaji Isa wrote:
>
> I want to create topology and coordinate file using ANTECHAMBER. When
> I run the below command
> antechamber -i 50_N.pdb -fi pdb -o 50.mol2 -fo mol2 -c bcc -s 2
>
> It gives the below error
>
>
>
> ---Judge bond type for Residue 1 with ID of 40 and Name of SUS ---
>
> 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
It's certainly worth upgrading to the current version of AmberTools. In
particular, input checking for antechamber is much improved. There are many
ways in which an arbitrary pdb file can fail in antechamber, and some of the
more common ones are now flagged.
....dac
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Received on Sat Jun 24 2017 - 06:00:04 PDT
