[gmx-users] Problem with adding New peptide Terminus

[Justin Lemkul]

On 9/23/19 9:48 PM, Neena Susan Eappen wrote:
> Hello gromacs users,
>
> I was trying to add a modified C-terminus for my peptide, an amide group at the C-terminus with a protonated carbonyl oxygen,  formula here [https://r2.res.outlook.com/owa/prem/images/photo_16x16.png] C_Terminus.png<https://utoronto-my.sharepoint.com/:i:/g/personal/neena_susaneappen_mail_utoronto_ca/EWtAhMdjXqxChGRZXWO7yjABHtyWUw-KALmjzH5iHGpEcA>
>
> I edited the tdb in the following way
>
> [ protonatedamide ]
> [ replace ]
> C CT5 opls_968 12.011   0.641
> O O1  opls_967 15.9994 -0.188
> [ add ]
> 1 1 NT CT5 O1           CA
>               opls_237 14.0067   -0.76
> 2 3 HT NT CT5 CA
>                opls_240 1.008       0.38
> 1 2 HO1 O1 CT5 CA
>                opls_966 1.008       0.547
> [ bonds ]
> HO1        O1
> NT           CT5
> HT           N
>
> I got an error message saying C atom in the input file does not correspond to topology database.
> I do not understand why I got this error message.

Please provide the full, exact error message that you got from pdb2gmx.

-Justin

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Justin A. Lemkul, Ph.D.
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