Re: [AMBER] SEP parameter with ff15ipq

From: vadiraj kurdekar <>
Date: Fri, 26 Aug 2016 04:43:22 +0000 (UTC)

Thanks, David Case and David Cerutti

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.

    On Friday, 26 August 2016 10:10 AM, vadiraj kurdekar <> wrote:

  With Regards, Vadiraj Kurdekar,Research Scholar, Pharmacy Dept.,
Birla Institute of Technology and Science-Pilani,
Pilani Campus, 
Rajasthan, PIN: 333031India.Mobile: + 91 9460763664

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    On Thursday, 25 August 2016 7:03 PM, David A Case <> wrote:

 On Thu, Aug 25, 2016, vadiraj kurdekar wrote:

> 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.ff15ipq
> leaprc.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.

The phosaa10 set was originally derived to be similar to ff99SB.  These models
should also work with ff14SB, although one may have to check for some
additional atom types that were added during the ff99SB -> ff14SB transition.

The charge and non-bonded model for ff14ipq and ff15ipq is rather different,
and so would not really be obviously compatible with phosaa10.  You can try
things out and see what happens, but you should realize that you are making a
new force field model.  Unless you are sure that you need ff15ipq for the rest
of the protein, I'd recommend using the combination of ff14SB and phosaa10.



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