[gmx-users] Problem with adding New peptide Terminus

Neena Susan Eappen neena.susaneappen at mail.utoronto.ca
Tue Sep 24 03:48:19 CEST 2019

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 let me know where I am going wrong.

Thank you,

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