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

From: Bill Ross <>
Date: Wed, 31 Oct 2018 02:30:25 -0700

Coming on this cold with a Sherlock Holmes approach and vestigial
awareness of chemistry (i.e. Dave's issue and your response), an obvious
possibility is that the frcmod.ff14SB file you added the params to is
not the one you are loading. Try listing the param in leap, or some
addition or deletion experiment to prove to yourself that you are
loading the right file, then burn this message and fly into the night. :-)


On 10/31/18 2:13 AM, Rajbinder Kaur Virk wrote:
> Hello
> 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:
> Angle
> 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
>> _______________________________________________
>> AMBER mailing list

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Received on Wed Oct 31 2018 - 03:00:02 PDT
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