Re: [AMBER] tleap gamma-carboxyglutamic acid linkage error

From: Rajbinder Kaur Virk <>
Date: Wed, 31 Oct 2018 14:43:58 +0530


This missing parameters is probably due the presence of gamma glutamic acid
as one of the amino acid in the peptide and it is forming a gamma linkage
as peptide bond. As discussed earlier, I tried to make .lib file, after
saving by xleap, the pdb seems to be right but prmtop and inpcrd files are
not being saved.

Following changes were made in the frcmod.ff14SB file:
O2-C -N 72.7 120.63
CT-O2-C-N 10.5 180. 2.

Please provide some suggestions....we are really stuck. Thank you

Thank you
With regards
Rajbinder Kaur Virk

On Wed, Oct 31, 2018 at 7:11 AM David Case <> wrote:

> On Tue, Oct 30, 2018, Rajbinder Kaur Virk wrote:
> >
> > Could not find angle parameter: O2 - C - N
> >
> > thereafter i tried to provide the required parameters in the .dat file
> > itself (frcmod.ff14SB), still the parameter are not being recognized and
> > the error persists.
> Can you show the exact changes to the frcmod.ff14SB file you made, plus all
> the commands you gave to tleap?
> As an aside, you should generally not edit frcmod.ff14SB itself, but rather
> make a new frcmod file--that way you won't mess up other runs that expect
> to
> have the un-modified frcmod.ff14SB file.
> Second aside: there are indeed no O2-C-N angles in ordinary proteins. Are
> you
> sure you have correct atom types?
> ....dac
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> AMBER mailing list

*With regards*
*Rajbinder Kaur Virk*
*Research Scholar *
*Department of Biophysics*
*Panjab University *
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Received on Wed Oct 31 2018 - 02:30:02 PDT
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