Re: [AMBER] SEP parameter with ff15ipq

From: Carlos Simmerling <>
Date: Fri, 26 Aug 2016 09:35:52 -0400

sorry I didn't see this right away, it went to my spam folder.
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I agree with the previous responses - you should be extra cautious of
mixing charge models, and certainly it will make it difficult to compare
the results with SEP from those using the ff15ipq standard serine. I'm not
aware of any nonstandard amino acids for the ff15ipq model.

On Thu, Aug 25, 2016 at 3:08 AM, vadiraj kurdekar <>

> Hi,
> I am working with peptide simulation which contains phospho serine
> followed by proline. when I generate topology file with tleap from
> ambertool16 I am getting an error "Could not find angle parameter: O - C -
> TN"
> I am using following forcefield parameter file in tleap
> leaprc.protein.ff15ipqleaprc.water.spceb
> leaprc.phosaa10
> however this works fine if i use leaprc.ff14ipq and leaprc.phosaa10. It
> looks like there is missing parameter for amide bond between SEP and
> proline.
> pls help me to add this missing parameter or let me know if it is ok to
> borrow it from ff14ipq.
> Regards,
> Vadiraj Kurdekar,
> The Centre for Chemical Biology and Therapeutics (CCBT),
> Institute for Stem Cell Biology and Regenerative Medicine (InStem),
> National Centre for Biological Sciences,
> GKVK, Bellary Road,Bangalore 560065, India.
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Received on Fri Aug 26 2016 - 07:00:02 PDT
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