Re: [AMBER] The error information

From: Bill Ross <>
Date: Wed, 3 Mar 2010 17:47:04 -0800 (PST)

> When I used tleap to generate the prmtop and inpcrd files for one enzyme, I
> got some error like that:
> 1-4: angle 4030 4031 duplicates bond ('triangular' bond) or angle ('square'
> bond)
> 1-4: angle 4029 4031 duplicates bond ('triangular' bond) or angle ('square'
> bond)
> 1-4: angle 4029 4030 duplicates bond ('triangular' bond) or angle ('square'
> bond)

I think these are warnings rather than errors. They suggest your model
has either a triangle of 3 bonded atoms, or a square formed by 4 atoms
bonded together. You may want to look at those atoms in xleap to see if
there is an extra bond in that region.

> Building improper torsion parameters.
> old PREP-specified impropers:
> <DMA 255>: CA OXT C O
> <DMA 255>: NE NH1 CZ NH2
> <DMA 255>: CD CZ NE HE
> <DMA 255>: CZ CT1 NH1 HH12
> <DMA 255>: CZ HH21 NH2 HH22

If you loadamberprep, the IMPROPER section is remembered and printed
out at this point to allow you to compare with the count of impropers
actually applied. Note that the IMPROPER section is only used for this
purpose and no longer is used for assigning impropers in Amber.

> Besides, here is a non-standard residue in the enzyme, for which I have
> developed a specific prepin file. It is a methyl arginine. It is weird that
> the parameter is required for the angle CA - CT - N2, which doesn't exist in
> the methyl arginine. Did that mean the parameter file I wrote was wrong?

I wonder if you have an extra bond in your residue definition.


AMBER mailing list
Received on Wed Mar 03 2010 - 18:00:03 PST
Custom Search