Re: [AMBER] Error while creation topology and coordinate files in tleap

From: David A Case <>
Date: Wed, 18 Jan 2017 15:32:50 -0500

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

AMBER mailing list
Received on Wed Jan 18 2017 - 13:00:03 PST
Custom Search