On Wed, Jan 18, 2017, Manjula Saravanan wrote:
> WARNING: There is a bond of 10.545950 angstroms between:
> ------- .R<EST 631>.A<C15 16> and .R<EST 631>.A<C17 18>
> WARNING: There is a bond of 6.708769 angstroms between:
> ------- .R<EST 631>.A<C11 12> and .R<EST 631>.A<C13 14>
> WARNING: There is a bond of 4.697628 angstroms between:
> ------- .R<EST 631>.A<C6 7> and .R<EST 631>.A<C8 9>
These are pretty straightforward messages: you need to check your input pdb
file to see if there are missing or incorrect coordinates.
> Could not find angle parameter: c3 - oh - c2
This is a pretty odd combination, but may be correct. Did you run parmchk2
after running antechamber? It should have provided you with a frcmod file
that would have that combination, if it exists in your molecules.
> 1-4: angle 3989 4003 duplicates bond ('triangular' bond) or angle ('square'
> bond)
This might or might not be problematic: do you have three- or four-member
rings in your structure? If not, there might be something wrong.
...good luck...dac
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Received on Wed Jan 18 2017 - 13:00:03 PST
